Data items in the ATOM_SITE category record details about the atom sites in a macromolecular crystal structure, such as the positional coordinates, atomic displacement parameters, magnetic moments and directions. The data items for describing anisotropic atomic displacement factors are only used if the corresponding items are not given in the ATOM_SITE_ANISOTROP category.
Mandatory: no
Keys: _atom_site.id
Groups: inclusive_group atom_group
Examples:
| Example | Detail |
|---|---|
loop_
_atom_site.group_PDB
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_comp_id
_atom_site.label_asym_id
_atom_site.label_seq_id
_atom_site.label_alt_id
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.footnote_id
_atom_site.auth_seq_id
_atom_site.id
ATOM N N VAL A 11 . 25.369 30.691 11.795 1.00 17.93 . 11 1
ATOM C CA VAL A 11 . 25.970 31.965 12.332 1.00 17.75 . 11 2
ATOM C C VAL A 11 . 25.569 32.010 13.808 1.00 17.83 . 11 3
ATOM O O VAL A 11 . 24.735 31.190 14.167 1.00 17.53 . 11 4
ATOM C CB VAL A 11 . 25.379 33.146 11.540 1.00 17.66 . 11 5
ATOM C CG1 VAL A 11 . 25.584 33.034 10.030 1.00 18.86 . 11 6
ATOM C CG2 VAL A 11 . 23.933 33.309 11.872 1.00 17.12 . 11 7
ATOM N N THR A 12 . 26.095 32.930 14.590 1.00 18.97 4 12 8
ATOM C CA THR A 12 . 25.734 32.995 16.032 1.00 19.80 4 12 9
ATOM C C THR A 12 . 24.695 34.106 16.113 1.00 20.92 4 12 10
ATOM O O THR A 12 . 24.869 35.118 15.421 1.00 21.84 4 12 11
ATOM C CB THR A 12 . 26.911 33.346 17.018 1.00 20.51 4 12 12
ATOM O OG1 THR A 12 3 27.946 33.921 16.183 0.50 20.29 4 12 13
ATOM O OG1 THR A 12 4 27.769 32.142 17.103 0.50 20.59 4 12 14
ATOM C CG2 THR A 12 3 27.418 32.181 17.878 0.50 20.47 4 12 15
ATOM C CG2 THR A 12 4 26.489 33.778 18.426 0.50 20.00 4 12 16
ATOM N N ILE A 13 . 23.664 33.855 16.884 1.00 22.08 . 13 17
ATOM C CA ILE A 13 . 22.623 34.850 17.093 1.00 23.44 . 13 18
ATOM C C ILE A 13 . 22.657 35.113 18.610 1.00 25.77 . 13 19
ATOM O O ILE A 13 . 23.123 34.250 19.406 1.00 26.28 . 13 20
ATOM C CB ILE A 13 . 21.236 34.463 16.492 1.00 22.67 . 13 21
ATOM C CG1 ILE A 13 . 20.478 33.469 17.371 1.00 22.14 . 13 22
ATOM C CG2 ILE A 13 . 21.357 33.986 15.016 1.00 21.75 . 13 23
# - - - - data truncated for brevity - - - -
HETATM C C1 APS C . 1 4.171 29.012 7.116 0.58 17.27 1 300 101
HETATM C C2 APS C . 1 4.949 27.758 6.793 0.58 16.95 1 300 102
HETATM O O3 APS C . 1 4.800 26.678 7.393 0.58 16.85 1 300 103
HETATM N N4 APS C . 1 5.930 27.841 5.869 0.58 16.43 1 300 104
# - - - - data truncated for brevity - - - -
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
Category: atom_site
Mandatory: no
Sub-category: matrix
The [1][1] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sumi[sumj(Bij hi hj a*i a*j)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred.
Type: float
Type conditions: esd
Units: 8pi2_angstroms_squared
Related items: _atom_site.aniso_B[1][1]_esd (associated_esd) _atom_site.aniso_U[1][1] (conversion_constant) _atom_site_anisotrop.U[1][1] (conversion_constant) _atom_site.aniso_U[1][1] (alternate_exclusive) _atom_site_anisotrop.B[1][1] (alternate_exclusive) _atom_site_anisotrop.U[1][1] (alternate_exclusive)
Category: atom_site
Mandatory: no
Sub-category: matrix
The standard uncertainty (estimated standard deviation) of _atom_site.aniso_B[1][1].
Type: float
Units: 8pi2_angstroms_squared
Related items: _atom_site.aniso_B[1][1] (associated_value) _atom_site.aniso_U[1][1]_esd (conversion_constant) _atom_site_anisotrop.U[1][1]_esd (conversion_constant) _atom_site.aniso_U[1][1]_esd (alternate_exclusive) _atom_site_anisotrop.B[1][1]_esd (alternate_exclusive) _atom_site_anisotrop.U[1][1]_esd (alternate_exclusive)
Category: atom_site
Mandatory: no
Sub-category: matrix
The [1][2] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sumi[sumj(Bij hi hj a*i a*j)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred.
Type: float
Type conditions: esd
Units: 8pi2_angstroms_squared
Related items: _atom_site.aniso_B[1][2]_esd (associated_esd) _atom_site.aniso_U[1][2] (conversion_constant) _atom_site_anisotrop.U[1][2] (conversion_constant) _atom_site.aniso_U[1][2] (alternate_exclusive) _atom_site_anisotrop.B[1][2] (alternate_exclusive) _atom_site_anisotrop.U[1][2] (alternate_exclusive)
Category: atom_site
Mandatory: no
Sub-category: matrix
The standard uncertainty (estimated standard deviation) of _atom_site.aniso_B[1][2].
Type: float
Units: 8pi2_angstroms_squared
Related items: _atom_site.aniso_B[1][2] (associated_value) _atom_site.aniso_U[1][2]_esd (conversion_constant) _atom_site_anisotrop.U[1][2]_esd (conversion_constant) _atom_site.aniso_U[1][2]_esd (alternate_exclusive) _atom_site_anisotrop.B[1][2]_esd (alternate_exclusive) _atom_site_anisotrop.U[1][2]_esd (alternate_exclusive)
Category: atom_site
Mandatory: no
Sub-category: matrix
The [1][3] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sumi[sumj(Bij hi hj a*i a*j)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred.
Type: float
Type conditions: esd
Units: 8pi2_angstroms_squared
Related items: _atom_site.aniso_B[1][3]_esd (associated_esd) _atom_site.aniso_U[1][3] (conversion_constant) _atom_site_anisotrop.U[1][3] (conversion_constant) _atom_site.aniso_U[1][3] (alternate_exclusive) _atom_site_anisotrop.B[1][3] (alternate_exclusive) _atom_site_anisotrop.U[1][3] (alternate_exclusive)
Category: atom_site
Mandatory: no
Sub-category: matrix
The standard uncertainty (estimated standard deviation) of _atom_site.aniso_B[1][3].
Type: float
Units: 8pi2_angstroms_squared
Related items: _atom_site.aniso_B[1][3] (associated_value) _atom_site.aniso_U[1][3]_esd (conversion_constant) _atom_site_anisotrop.U[1][3]_esd (conversion_constant) _atom_site.aniso_U[1][3]_esd (alternate_exclusive) _atom_site_anisotrop.B[1][3]_esd (alternate_exclusive) _atom_site_anisotrop.U[1][3]_esd (alternate_exclusive)
Category: atom_site
Mandatory: no
The [2][2] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sumi[sumj(Bij hi hj a*i a*j)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred.
Type: float
Type conditions: esd
Units: 8pi2_angstroms_squared
Related items: _atom_site.aniso_B[2][2]_esd (associated_esd) _atom_site.aniso_U[2][2] (conversion_constant) _atom_site_anisotrop.U[2][2] (conversion_constant) _atom_site.aniso_U[2][2] (alternate_exclusive) _atom_site_anisotrop.B[2][2] (alternate_exclusive) _atom_site_anisotrop.U[2][2] (alternate_exclusive)
Category: atom_site
Mandatory: no
Sub-category: matrix
The standard uncertainty (estimated standard deviation) of _atom_site.aniso_B[2][2].
Type: float
Units: 8pi2_angstroms_squared
Related items: _atom_site.aniso_B[2][2] (associated_value) _atom_site.aniso_U[2][2]_esd (conversion_constant) _atom_site_anisotrop.U[2][2]_esd (conversion_constant) _atom_site.aniso_U[2][2]_esd (alternate_exclusive) _atom_site_anisotrop.B[2][2]_esd (alternate_exclusive) _atom_site_anisotrop.U[2][2]_esd (alternate_exclusive)
Category: atom_site
Mandatory: no
Sub-category: matrix
The [2][3] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sumi[sumj(Bij hi hj a*i a*j)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred.
Type: float
Type conditions: esd
Units: 8pi2_angstroms_squared
Related items: _atom_site.aniso_B[2][3]_esd (associated_esd) _atom_site.aniso_U[2][3] (conversion_constant) _atom_site_anisotrop.U[2][3] (conversion_constant) _atom_site.aniso_U[2][3] (alternate_exclusive) _atom_site_anisotrop.B[2][3] (alternate_exclusive) _atom_site_anisotrop.U[2][3] (alternate_exclusive)
Category: atom_site
Mandatory: no
Sub-category: matrix
The standard uncertainty (estimated standard deviation) of _atom_site.aniso_B[2][3].
Type: float
Units: 8pi2_angstroms_squared
Related items: _atom_site.aniso_B[2][3] (associated_value) _atom_site.aniso_U[2][3]_esd (conversion_constant) _atom_site_anisotrop.U[2][3]_esd (conversion_constant) _atom_site.aniso_U[2][3]_esd (alternate_exclusive) _atom_site_anisotrop.B[2][3]_esd (alternate_exclusive) _atom_site_anisotrop.U[2][3]_esd (alternate_exclusive)
Category: atom_site
Mandatory: no
Sub-category: matrix
The [3][3] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sumi[sumj(Bij hi hj a*i a*j)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred.
Type: float
Type conditions: esd
Units: 8pi2_angstroms_squared
Related items: _atom_site.aniso_B[3][3]_esd (associated_esd) _atom_site.aniso_U[3][3] (conversion_constant) _atom_site_anisotrop.U[3][3] (conversion_constant) _atom_site.aniso_U[3][3] (alternate_exclusive) _atom_site_anisotrop.B[3][3] (alternate_exclusive) _atom_site_anisotrop.U[3][3] (alternate_exclusive)
Category: atom_site
Mandatory: no
Sub-category: matrix
The standard uncertainty (estimated standard deviation) of _atom_site.aniso_B[3][3].
Type: float
Units: 8pi2_angstroms_squared
Related items: _atom_site.aniso_B[3][3] (associated_value) _atom_site.aniso_U[3][3]_esd (conversion_constant) _atom_site_anisotrop.U[3][3]_esd (conversion_constant) _atom_site.aniso_U[3][3]_esd (alternate_exclusive) _atom_site_anisotrop.B[3][3]_esd (alternate_exclusive) _atom_site_anisotrop.U[3][3]_esd (alternate_exclusive)
Category: atom_site
Mandatory: no
Ratio of the maximum to minimum principal axes of displacement (thermal) ellipsoids.
Type: float
Related item: _atom_site_anisotrop.ratio (alternate_exclusive)
Range: [1.0, .] [1.0, 1.0]
Category: atom_site
Mandatory: no
Sub-category: matrix
The [1][1] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi2 sumi[sumj(Uij hi hj a*i a*j)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row.
Type: float
Type conditions: esd
Units: angstroms_squared
Related items: _atom_site.aniso_U[1][1]_esd (associated_esd) _atom_site.aniso_B[1][1] (conversion_constant) _atom_site_anisotrop.B[1][1] (conversion_constant) _atom_site.aniso_B[1][1] (alternate_exclusive) _atom_site_anisotrop.B[1][1] (alternate_exclusive) _atom_site_anisotrop.U[1][1] (alternate_exclusive)
Category: atom_site
Mandatory: no
Sub-category: matrix
The standard uncertainty (estimated standard deviation) of _atom_site.aniso_U[1][1].
Type: float
Units: angstroms_squared
Related items: _atom_site.aniso_U[1][1] (associated_value) _atom_site.aniso_B[1][1]_esd (conversion_constant) _atom_site_anisotrop.B[1][1]_esd (conversion_constant) _atom_site.aniso_B[1][1]_esd (alternate_exclusive) _atom_site_anisotrop.B[1][1]_esd (alternate_exclusive) _atom_site_anisotrop.U[1][1]_esd (alternate_exclusive)
Category: atom_site
Mandatory: no
The [1][2] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi2 sumi[sumj(Uij hi hj a*i a*j)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row.
Type: float
Type conditions: esd
Units: angstroms_squared
Related items: _atom_site.aniso_U[1][2]_esd (associated_esd) _atom_site.aniso_B[1][2] (conversion_constant) _atom_site_anisotrop.B[1][2] (conversion_constant) _atom_site.aniso_B[1][2] (alternate_exclusive) _atom_site_anisotrop.B[1][2] (alternate_exclusive) _atom_site_anisotrop.U[1][2] (alternate_exclusive)
Category: atom_site
Mandatory: no
Sub-category: matrix
The standard uncertainty (estimated standard deviation) of _atom_site.aniso_U[1][2].
Type: float
Units: angstroms_squared
Related items: _atom_site.aniso_U[1][2] (associated_value) _atom_site.aniso_B[1][2]_esd (conversion_constant) _atom_site_anisotrop.B[1][2]_esd (conversion_constant) _atom_site.aniso_B[1][2]_esd (alternate_exclusive) _atom_site_anisotrop.B[1][2]_esd (alternate_exclusive) _atom_site_anisotrop.U[1][2]_esd (alternate_exclusive)
Category: atom_site
Mandatory: no
Sub-category: matrix
The [1][3] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi2 sumi[sumj(Uij hi hj a*i a*j)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row.
Type: float
Type conditions: esd
Units: angstroms_squared
Related items: _atom_site.aniso_U[1][3]_esd (associated_esd) _atom_site.aniso_B[1][3] (conversion_constant) _atom_site_anisotrop.B[1][3] (conversion_constant) _atom_site.aniso_B[1][3] (alternate_exclusive) _atom_site_anisotrop.B[1][3] (alternate_exclusive) _atom_site_anisotrop.U[1][3] (alternate_exclusive)
Category: atom_site
Mandatory: no
Sub-category: matrix
The standard uncertainty (estimated standard deviation) of _atom_site.aniso_U[1][3].
Type: float
Units: angstroms_squared
Related items: _atom_site.aniso_U[1][3] (associated_value) _atom_site.aniso_B[1][3]_esd (conversion_constant) _atom_site_anisotrop.B[1][3]_esd (conversion_constant) _atom_site.aniso_B[1][3]_esd (alternate_exclusive) _atom_site_anisotrop.B[1][3]_esd (alternate_exclusive) _atom_site_anisotrop.U[1][3]_esd (alternate_exclusive)
Category: atom_site
Mandatory: no
Sub-category: matrix
The [2][2] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi2 sumi[sumj(Uij hi hj a*i a*j)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row.
Type: float
Type conditions: esd
Units: angstroms_squared
Related items: _atom_site.aniso_U[2][2]_esd (associated_esd) _atom_site.aniso_B[2][2] (conversion_constant) _atom_site_anisotrop.B[2][2] (conversion_constant) _atom_site.aniso_B[2][2] (alternate_exclusive) _atom_site_anisotrop.B[2][2] (alternate_exclusive) _atom_site_anisotrop.U[2][2] (alternate_exclusive)
Category: atom_site
Mandatory: no
Sub-category: matrix
The standard uncertainty (estimated standard deviation) of _atom_site.aniso_U[2][2].
Type: float
Units: angstroms_squared
Related items: _atom_site.aniso_U[2][2] (associated_value) _atom_site.aniso_B[2][2]_esd (conversion_constant) _atom_site_anisotrop.B[2][2]_esd (conversion_constant) _atom_site.aniso_B[2][2]_esd (alternate_exclusive) _atom_site_anisotrop.B[2][2]_esd (alternate_exclusive) _atom_site_anisotrop.U[2][2]_esd (alternate_exclusive)
Category: atom_site
Mandatory: no
Sub-category: matrix
The [2][3] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi2 sumi[sumj(Uij hi hj a*i a*j)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row.
Type: float
Type conditions: esd
Units: angstroms_squared
Related items: _atom_site.aniso_U[2][3]_esd (associated_esd) _atom_site.aniso_B[2][3] (conversion_constant) _atom_site_anisotrop.B[2][3] (conversion_constant) _atom_site.aniso_B[2][3] (alternate_exclusive) _atom_site_anisotrop.B[2][3] (alternate_exclusive) _atom_site_anisotrop.U[2][3] (alternate_exclusive)
Category: atom_site
Mandatory: no
Sub-category: matrix
The standard uncertainty (estimated standard deviation) of _atom_site.aniso_U[2][3].
Type: float
Units: angstroms_squared
Related items: _atom_site.aniso_U[2][3] (associated_value) _atom_site.aniso_B[2][3]_esd (conversion_constant) _atom_site_anisotrop.B[2][3]_esd (conversion_constant) _atom_site.aniso_B[2][3]_esd (alternate_exclusive) _atom_site_anisotrop.B[2][3]_esd (alternate_exclusive) _atom_site_anisotrop.U[2][3]_esd (alternate_exclusive)
Category: atom_site
Mandatory: no
Sub-category: matrix
The [3][3] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi2 sumi[sumj(Uij hi hj a*i a*j)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row.
Type: float
Type conditions: esd
Units: angstroms_squared
Related items: _atom_site.aniso_U[3][3]_esd (associated_esd) _atom_site.aniso_B[3][3] (conversion_constant) _atom_site_anisotrop.B[3][3] (conversion_constant) _atom_site.aniso_B[3][3] (alternate_exclusive) _atom_site_anisotrop.B[3][3] (alternate_exclusive) _atom_site_anisotrop.U[3][3] (alternate_exclusive)
Category: atom_site
Mandatory: no
Sub-category: matrix
The standard uncertainty (estimated standard deviation) of _atom_site.aniso_U[3][3].
Type: float
Units: angstroms_squared
Related items: _atom_site.aniso_U[3][3] (associated_value) _atom_site.aniso_B[3][3]_esd (conversion_constant) _atom_site_anisotrop.B[3][3]_esd (conversion_constant) _atom_site.aniso_B[3][3]_esd (alternate_exclusive) _atom_site_anisotrop.B[3][3]_esd (alternate_exclusive) _atom_site_anisotrop.U[3][3]_esd (alternate_exclusive)
Category: atom_site
Mandatory: no
The number of hydrogen atoms attached to the atom at this site excluding any hydrogen atoms for which coordinates (measured or calculated) are given.
Alias: _atom_site_attached_hydrogens (cif_core.dic, 2.0.1)
Type: int
Range: [8, 8] [0, 8] [0, 0]
Examples:
| Example | Detail |
|---|---|
2 |
water oxygen |
1 |
hydroxyl oxygen |
4 |
ammonium nitrogen |
| Name | Category | Mandatory |
|---|---|---|
| _atom_site.auth_asym_id | atom_site | yes |
| _geom_angle.atom_site_auth_asym_id_1 | geom_angle | no |
| _geom_angle.atom_site_auth_asym_id_2 | geom_angle | no |
| _geom_angle.atom_site_auth_asym_id_3 | geom_angle | no |
| _geom_bond.atom_site_auth_asym_id_1 | geom_bond | no |
| _geom_bond.atom_site_auth_asym_id_2 | geom_bond | no |
| _geom_contact.atom_site_auth_asym_id_1 | geom_contact | no |
| _geom_contact.atom_site_auth_asym_id_2 | geom_contact | no |
| _geom_hbond.atom_site_auth_asym_id_A | geom_hbond | no |
| _geom_hbond.atom_site_auth_asym_id_D | geom_hbond | no |
| _geom_hbond.atom_site_auth_asym_id_H | geom_hbond | no |
| _geom_torsion.atom_site_auth_asym_id_1 | geom_torsion | no |
| _geom_torsion.atom_site_auth_asym_id_2 | geom_torsion | no |
| _geom_torsion.atom_site_auth_asym_id_3 | geom_torsion | no |
| _geom_torsion.atom_site_auth_asym_id_4 | geom_torsion | no |
| _struct_conf.beg_auth_asym_id | struct_conf | no |
| _struct_conf.end_auth_asym_id | struct_conf | no |
| _struct_conn.ptnr1_auth_asym_id | struct_conn | no |
| _struct_conn.ptnr2_auth_asym_id | struct_conn | no |
| _struct_mon_nucl.auth_asym_id | struct_mon_nucl | no |
| _struct_mon_prot.auth_asym_id | struct_mon_prot | no |
| _struct_mon_prot_cis.auth_asym_id | struct_mon_prot_cis | no |
| _struct_ncs_dom_lim.beg_auth_asym_id | struct_ncs_dom_lim | no |
| _struct_ncs_dom_lim.end_auth_asym_id | struct_ncs_dom_lim | no |
| _struct_sheet_range.beg_auth_asym_id | struct_sheet_range | no |
| _struct_sheet_range.end_auth_asym_id | struct_sheet_range | no |
| _struct_site_gen.auth_asym_id | struct_site_gen | no |
Sub-category: mm_atom_site_auth_label
An alternative identifier for _atom_site.label_asym_id that may be provided by an author in order to match the identification used in the publication that describes the structure.
Type: code
Child / Parent relations:
| Name | Category | Mandatory |
|---|---|---|
| _atom_site.auth_atom_id | atom_site | no |
| _geom_angle.atom_site_auth_atom_id_1 | geom_angle | no |
| _geom_angle.atom_site_auth_atom_id_2 | geom_angle | no |
| _geom_angle.atom_site_auth_atom_id_3 | geom_angle | no |
| _geom_bond.atom_site_auth_atom_id_1 | geom_bond | no |
| _geom_bond.atom_site_auth_atom_id_2 | geom_bond | no |
| _geom_contact.atom_site_auth_atom_id_1 | geom_contact | no |
| _geom_contact.atom_site_auth_atom_id_2 | geom_contact | no |
| _geom_hbond.atom_site_auth_atom_id_A | geom_hbond | no |
| _geom_hbond.atom_site_auth_atom_id_D | geom_hbond | no |
| _geom_hbond.atom_site_auth_atom_id_H | geom_hbond | no |
| _geom_torsion.atom_site_auth_atom_id_1 | geom_torsion | no |
| _geom_torsion.atom_site_auth_atom_id_2 | geom_torsion | no |
| _geom_torsion.atom_site_auth_atom_id_3 | geom_torsion | no |
| _geom_torsion.atom_site_auth_atom_id_4 | geom_torsion | no |
| _struct_conn.ptnr1_auth_atom_id | struct_conn | no |
| _struct_conn.ptnr2_auth_atom_id | struct_conn | no |
| _struct_sheet_hbond.range_1_beg_auth_atom_id | struct_sheet_hbond | no |
| _struct_sheet_hbond.range_1_end_auth_atom_id | struct_sheet_hbond | no |
| _struct_sheet_hbond.range_2_beg_auth_atom_id | struct_sheet_hbond | no |
| _struct_sheet_hbond.range_2_end_auth_atom_id | struct_sheet_hbond | no |
| _struct_site_gen.auth_atom_id | struct_site_gen | no |
Sub-category: mm_atom_site_auth_label
An alternative identifier for _atom_site.label_atom_id that may be provided by an author in order to match the identification used in the publication that describes the structure.
Type: atcode
Child / Parent relations:
| Name | Category | Mandatory |
|---|---|---|
| _atom_site.auth_comp_id | atom_site | no |
| _geom_angle.atom_site_auth_comp_id_1 | geom_angle | no |
| _geom_angle.atom_site_auth_comp_id_2 | geom_angle | no |
| _geom_angle.atom_site_auth_comp_id_3 | geom_angle | no |
| _geom_bond.atom_site_auth_comp_id_1 | geom_bond | no |
| _geom_bond.atom_site_auth_comp_id_2 | geom_bond | no |
| _geom_contact.atom_site_auth_comp_id_1 | geom_contact | no |
| _geom_contact.atom_site_auth_comp_id_2 | geom_contact | no |
| _geom_hbond.atom_site_auth_comp_id_A | geom_hbond | no |
| _geom_hbond.atom_site_auth_comp_id_D | geom_hbond | no |
| _geom_hbond.atom_site_auth_comp_id_H | geom_hbond | no |
| _geom_torsion.atom_site_auth_comp_id_1 | geom_torsion | no |
| _geom_torsion.atom_site_auth_comp_id_2 | geom_torsion | no |
| _geom_torsion.atom_site_auth_comp_id_3 | geom_torsion | no |
| _geom_torsion.atom_site_auth_comp_id_4 | geom_torsion | no |
| _struct_conf.beg_auth_comp_id | struct_conf | no |
| _struct_conf.end_auth_comp_id | struct_conf | no |
| _struct_conn.ptnr1_auth_comp_id | struct_conn | no |
| _struct_conn.ptnr2_auth_comp_id | struct_conn | no |
| _struct_mon_nucl.auth_comp_id | struct_mon_nucl | no |
| _struct_mon_prot.auth_comp_id | struct_mon_prot | no |
| _struct_mon_prot_cis.auth_comp_id | struct_mon_prot_cis | no |
| _struct_ncs_dom_lim.beg_auth_comp_id | struct_ncs_dom_lim | no |
| _struct_ncs_dom_lim.end_auth_comp_id | struct_ncs_dom_lim | no |
| _struct_sheet_range.beg_auth_comp_id | struct_sheet_range | no |
| _struct_sheet_range.end_auth_comp_id | struct_sheet_range | no |
| _struct_site_gen.auth_comp_id | struct_site_gen | no |
Sub-category: mm_atom_site_auth_label
An alternative identifier for _atom_site.label_comp_id that may be provided by an author in order to match the identification used in the publication that describes the structure.
Type: code
Child / Parent relations:
| Name | Category | Mandatory |
|---|---|---|
| _atom_site.auth_seq_id | atom_site | no |
| _geom_angle.atom_site_auth_seq_id_1 | geom_angle | no |
| _geom_angle.atom_site_auth_seq_id_2 | geom_angle | no |
| _geom_angle.atom_site_auth_seq_id_3 | geom_angle | no |
| _geom_bond.atom_site_auth_seq_id_1 | geom_bond | no |
| _geom_bond.atom_site_auth_seq_id_2 | geom_bond | no |
| _geom_contact.atom_site_auth_seq_id_1 | geom_contact | no |
| _geom_contact.atom_site_auth_seq_id_2 | geom_contact | no |
| _geom_hbond.atom_site_auth_seq_id_A | geom_hbond | no |
| _geom_hbond.atom_site_auth_seq_id_D | geom_hbond | no |
| _geom_hbond.atom_site_auth_seq_id_H | geom_hbond | no |
| _geom_torsion.atom_site_auth_seq_id_1 | geom_torsion | no |
| _geom_torsion.atom_site_auth_seq_id_2 | geom_torsion | no |
| _geom_torsion.atom_site_auth_seq_id_3 | geom_torsion | no |
| _geom_torsion.atom_site_auth_seq_id_4 | geom_torsion | no |
| _struct_conf.beg_auth_seq_id | struct_conf | no |
| _struct_conf.end_auth_seq_id | struct_conf | no |
| _struct_conn.ptnr1_auth_seq_id | struct_conn | no |
| _struct_conn.ptnr2_auth_seq_id | struct_conn | no |
| _struct_mon_nucl.auth_seq_id | struct_mon_nucl | no |
| _struct_mon_prot.auth_seq_id | struct_mon_prot | no |
| _struct_mon_prot_cis.auth_seq_id | struct_mon_prot_cis | no |
| _struct_ncs_dom_lim.beg_auth_seq_id | struct_ncs_dom_lim | no |
| _struct_ncs_dom_lim.end_auth_seq_id | struct_ncs_dom_lim | no |
| _struct_sheet_hbond.range_1_beg_auth_seq_id | struct_sheet_hbond | no |
| _struct_sheet_hbond.range_1_end_auth_seq_id | struct_sheet_hbond | no |
| _struct_sheet_hbond.range_2_beg_auth_seq_id | struct_sheet_hbond | no |
| _struct_sheet_hbond.range_2_end_auth_seq_id | struct_sheet_hbond | no |
| _struct_sheet_range.beg_auth_seq_id | struct_sheet_range | no |
| _struct_sheet_range.end_auth_seq_id | struct_sheet_range | no |
| _struct_site_gen.auth_seq_id | struct_site_gen | no |
Sub-category: mm_atom_site_auth_label
An alternative identifier for _atom_site.label_seq_id that may be provided by an author in order to match the identification used in the publication that describes the structure. Note that this is not necessarily a number, that the values do not have to be positive, and that the value does not have to correspond to the value of _atom_site.label_seq_id. The value of _atom_site.label_seq_id is required to be a sequential list of positive integers. The author may assign values to _atom_site.auth_seq_id in any desired way. For instance, the values may be used to relate this structure to a numbering scheme in a homologous structure, including sequence gaps or insertion codes. Alternatively, a scheme may be used for a truncated polymer that maintains the numbering scheme of the full length polymer. In all cases, the scheme used here must match the scheme used in the publication that describes the structure.
Type: code
Child / Parent relations:
Category: atom_site
Mandatory: no
Equivalent isotropic atomic displacement parameter, Beq, in angstroms squared, calculated as the geometric mean of the anisotropic atomic displacement parameters. Beq = (Bi Bj Bk)1/3 Bn = the principal components of the orthogonalized Bij The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred.
Alias: _atom_site_B_equiv_geom_mean (cif_core.dic, 2.0.1)
Type: float
Type conditions: esd
Units: 8pi2_angstroms_squared
Related items: _atom_site.B_equiv_geom_mean_esd (associated_esd) _atom_site.U_equiv_geom_mean (conversion_constant)
Range: [0.0, .] [0.0, 0.0]
Category: atom_site
Mandatory: no
The standard uncertainty (estimated standard deviation) of _atom_site.B_equiv_geom_mean.
Type: float
Units: 8pi2_angstroms_squared
Related items: _atom_site.B_equiv_geom_mean (associated_value) _atom_site.U_equiv_geom_mean (conversion_constant)
Category: atom_site
Mandatory: no
Isotropic atomic displacement parameter, or equivalent isotropic atomic displacement parameter, Beq, calculated from the anisotropic displacement parameters. Beq = (1/3) sumi[sumj(Bij Ai Aj a*i a*j)] A = the real space cell lengths a* = the reciprocal space cell lengths Bij = 8 pi2 Uij Ref: Fischer, R. X. & Tillmanns, E. (1988). Acta Cryst. C44, 775-776. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred.
Alias: _atom_site_B_iso_or_equiv (cif_core.dic, 2.0.1)
Type: float
Type conditions: esd
Units: 8pi2_angstroms_squared
Related items: _atom_site.B_iso_or_equiv_esd (associated_esd) _atom_site.U_iso_or_equiv (conversion_constant)
Category: atom_site
Mandatory: no
The standard uncertainty (estimated standard deviation) of _atom_site.B_iso_or_equiv.
Type: float
Units: 8pi2_angstroms_squared
Related items: _atom_site.B_iso_or_equiv (associated_value) _atom_site.U_iso_or_equiv_esd (conversion_constant)
Category: atom_site
Mandatory: no
The _atom_site.id of the atom site to which the 'geometry-calculated' atom site is attached.
Alias: _atom_site_calc_attached_atom (cif_core.dic, 2.0.1)
Type: code
Category: atom_site
Mandatory: no
A standard code to signal whether the site coordinates have been determined from the intensities or calculated from the geometry of surrounding sites, or have been assigned dummy values. The abbreviation 'c' may be used in place of 'calc'.
Alias: _atom_site_calc_flag (cif_core.dic, 2.0.1)
Type: ucode
Enumeration values:
| Value | Detail |
|---|---|
d |
determined from experimental measurements |
calc |
calculated from molecular geometry |
c |
abbreviation for "calc" |
dum |
dummy site with meaningless coordinates |
Category: atom_site
Mandatory: no
Sub-category: cartesian_coordinate
The x atom-site coordinate in angstroms specified according to a set of orthogonal Cartesian axes related to the cell axes as specified by the description given in _atom_sites.Cartn_transform_axes.
Alias: _atom_site_Cartn_x (cif_core.dic, 2.0.1)
Type: float
Type conditions: esd
Units: angstroms
Dependent items: _atom_site.Cartn_y _atom_site.Cartn_z
Related item: _atom_site.Cartn_x_esd (associated_esd)
Category: atom_site
Mandatory: no
Sub-category: cartesian_coordinate_esd
The standard uncertainty (estimated standard deviation) of _atom_site.Cartn_x.
Type: float
Units: angstroms
Dependent items: _atom_site.Cartn_y_esd _atom_site.Cartn_z_esd
Related item: _atom_site.Cartn_x (associated_value)
Category: atom_site
Mandatory: no
Sub-category: cartesian_coordinate
The y atom-site coordinate in angstroms specified according to a set of orthogonal Cartesian axes related to the cell axes as specified by the description given in _atom_sites.Cartn_transform_axes.
Alias: _atom_site_Cartn_y (cif_core.dic, 2.0.1)
Type: float
Type conditions: esd
Units: angstroms
Dependent items: _atom_site.Cartn_x _atom_site.Cartn_z
Related item: _atom_site.Cartn_y_esd (associated_esd)
Category: atom_site
Mandatory: no
Sub-category: cartesian_coordinate_esd
The standard uncertainty (estimated standard deviation) of _atom_site.Cartn_y.
Type: float
Units: angstroms
Dependent items: _atom_site.Cartn_x_esd _atom_site.Cartn_z_esd
Related item: _atom_site.Cartn_y (associated_value)
Category: atom_site
Mandatory: no
Sub-category: cartesian_coordinate
The z atom-site coordinate in angstroms specified according to a set of orthogonal Cartesian axes related to the cell axes as specified by the description given in _atom_sites.Cartn_transform_axes.
Alias: _atom_site_Cartn_z (cif_core.dic, 2.0.1)
Type: float
Type conditions: esd
Units: angstroms
Dependent items: _atom_site.Cartn_x _atom_site.Cartn_y
Related item: _atom_site.Cartn_z_esd (associated_esd)
Category: atom_site
Mandatory: no
Sub-category: cartesian_coordinate_esd
The standard uncertainty (estimated standard deviation) of _atom_site.Cartn_z.
Type: float
Units: angstroms
Dependent items: _atom_site.Cartn_x_esd _atom_site.Cartn_y_esd
Related item: _atom_site.Cartn_z (associated_value)
Mandatory: no
This data item is a pointer to _chemical_conn_atom.number in the CHEMICAL_CONN_ATOM category.
Alias: _atom_site_chemical_conn_number (cif_core.dic, 2.0.1)
Category: atom_site
Mandatory: no
A description of the constraints applied to parameters at this site during refinement. See also _atom_site.refinement_flags and _refine.ls_number_constraints.
Alias: _atom_site_constraints (cif_core.dic, 2.0.1)
Type: line
Example:
pop=1.0-pop(Zn3)
Category: atom_site
Mandatory: no
A description of special aspects of this site. See also _atom_site.refinement_flags.
Alias: _atom_site_description (cif_core.dic, 2.0.1)
Type: text
Example:
Ag/Si disordered
Category: atom_site
Mandatory: no
A code which identifies a cluster of atoms that show long-range positional disorder but are locally ordered. Within each such cluster of atoms, _atom_site.disorder_group is used to identify the sites that are simultaneously occupied. This field is only needed if there is more than one cluster of disordered atoms showing independent local order. *** This data item would not in general be used in a macromolecular data block. ***
Alias: _atom_site_disorder_assembly (cif_core.dic, 2.0.1)
Type: code
Category: atom_site
Mandatory: no
A code which identifies a group of positionally disordered atom sites that are locally simultaneously occupied. Atoms that are positionally disordered over two or more sites (e.g. the hydrogen atoms of a methyl group that exists in two orientations) can be assigned to two or more groups. Sites belonging to the same group are simultaneously occupied, but those belonging to different groups are not. A minus prefix (e.g. '-1') is used to indicate sites disordered about a special position. *** This data item would not in general be used in a macromolecular data block. ***
Alias: _atom_site_disorder_group (cif_core.dic, 2.0.1)
Type: code
Default value: .
Mandatory: no
The value of _atom_site.footnote_id must match an ID specified by _atom_sites_footnote.id in the ATOM_SITES_FOOTNOTE list.
Category: atom_site
Mandatory: no
Sub-category: fractional_coordinate
The x coordinate of the atom-site position specified as a fraction of _cell.length_a.
Alias: _atom_site_fract_x (cif_core.dic, 2.0.1)
Type: float
Type conditions: esd
Dependent items: _atom_site.fract_y _atom_site.fract_z
Related item: _atom_site.fract_x_esd (associated_esd)
Category: atom_site
Mandatory: no
Sub-category: fractional_coordinate_esd
The standard uncertainty (estimated standard deviation) of _atom_site.fract_x.
Type: float
Dependent items: _atom_site.fract_y_esd _atom_site.fract_z_esd
Related item: _atom_site.fract_x (associated_value)
Category: atom_site
Mandatory: no
Sub-category: fractional_coordinate
The y coordinate of the atom-site position specified as a fraction of _cell.length_b.
Alias: _atom_site_fract_y (cif_core.dic, 2.0.1)
Type: float
Type conditions: esd
Dependent items: _atom_site.fract_x _atom_site.fract_z
Related item: _atom_site.fract_y_esd (associated_esd)
Category: atom_site
Mandatory: no
Sub-category: fractional_coordinate_esd
The standard uncertainty (estimated standard deviation) of _atom_site.fract_y.
Type: float
Dependent items: _atom_site.fract_x_esd _atom_site.fract_z_esd
Related item: _atom_site.fract_y (associated_value)
Category: atom_site
Mandatory: no
Sub-category: fractional_coordinate
The z coordinate of the atom-site position specified as a fraction of _cell.length_c.
Alias: _atom_site_fract_z (cif_core.dic, 2.0.1)
Type: float
Type conditions: esd
Dependent items: _atom_site.fract_x _atom_site.fract_y
Related item: _atom_site.fract_z_esd (associated_esd)
Category: atom_site
Mandatory: no
Sub-category: fractional_coordinate_esd
The standard uncertainty (estimated standard deviation) of _atom_site.fract_z.
Type: float
Dependent items: _atom_site.fract_x_esd _atom_site.fract_y_esd
Related item: _atom_site.fract_z (associated_value)
Category: atom_site
Mandatory: no
The group of atoms to which the atom site belongs. This data item is provided for compatibility with the original Protein Data Bank format, and only for that purpose.
Type: code
Enumeration values:
| Value | Detail |
|---|---|
ATOM |
|
HETATM |
| Name | Category | Mandatory |
|---|---|---|
| _atom_site.id | atom_site | yes |
| _atom_site_anisotrop.id | atom_site_anisotrop | yes |
| _geom_angle.atom_site_id_1 | geom_angle | yes |
| _geom_angle.atom_site_id_2 | geom_angle | yes |
| _geom_angle.atom_site_id_3 | geom_angle | yes |
| _geom_bond.atom_site_id_1 | geom_bond | yes |
| _geom_bond.atom_site_id_2 | geom_bond | yes |
| _geom_contact.atom_site_id_1 | geom_contact | yes |
| _geom_contact.atom_site_id_2 | geom_contact | yes |
| _geom_hbond.atom_site_id_A | geom_hbond | yes |
| _geom_hbond.atom_site_id_D | geom_hbond | yes |
| _geom_hbond.atom_site_id_H | geom_hbond | yes |
| _geom_torsion.atom_site_id_1 | geom_torsion | yes |
| _geom_torsion.atom_site_id_2 | geom_torsion | yes |
| _geom_torsion.atom_site_id_3 | geom_torsion | yes |
| _geom_torsion.atom_site_id_4 | geom_torsion | yes |
The value of _atom_site.id must uniquely identify a record in the ATOM_SITE list. Note that this item need not be a number; it can be any unique identifier. This data item was introduced to provide compatibility between small-molecule and macromolecular CIFs. In a small-molecule CIF, _atom_site_label is the identifier for the atom. In a macromolecular CIF, the atom identifier is the aggregate of _atom_site.label_alt_id, _atom_site.label_asym_id, _atom_site.label_atom_id, _atom_site.label_comp_id and _atom_site.label_seq_id. For the two types of files to be compatible, a formal identifier for the category had to be introduced that was independent of the different modes of identifying the atoms. For compatibility with older CIFs, _atom_site_label is aliased to _atom_site.id.
Alias: _atom_site_label (cif_core.dic, 2.0.1)
Type: code
Child / Parent relations:
Examples:
| Example | Detail |
|---|---|
5 |
|
C12 |
|
Ca3g28 |
|
Fe3+17 |
|
H*251 |
|
boron2a |
|
C_a_phe_83_a_0 |
|
Zn_Zn_301_A_0 |
Mandatory: yes
Sub-category: mm_atom_site_label
A component of the identifier for this atom site. For further details, see the definition of the ATOM_SITE_ALT category. This data item is a pointer to _atom_sites_alt.id in the ATOM_SITES_ALT category.
Mandatory: yes
Sub-category: mm_atom_site_label
A component of the identifier for this atom site. For further details, see the definition of the STRUCT_ASYM category. This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category.
Mandatory: yes
Sub-category: mm_atom_site_label
A component of the identifier for this atom site. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category.
Mandatory: yes
Sub-category: mm_atom_site_label
A component of the identifier for this atom site. This data item is a pointer to _chem_comp.id in the CHEM_COMP category.
Mandatory: yes
This data item is a pointer to _entity.id in the ENTITY category.
Mandatory: yes
This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category.
Category: atom_site
Mandatory: no
The fraction of the atom type present at this site. The sum of the occupancies of all the atom types at this site may not significantly exceed 1.0 unless it is a dummy site.
Alias: _atom_site_occupancy (cif_core.dic, 2.0.1)
Type: float
Type conditions: esd
Related item: _atom_site.occupancy_esd (associated_esd)
Default value: 1.0
Category: atom_site
Mandatory: no
The standard uncertainty (estimated standard deviation) of _atom_site.occupancy.
Type: float
Related item: _atom_site.occupancy (associated_value)
Category: atom_site
Mandatory: no
A description of restraints applied to specific parameters at this site during refinement. See also _atom_site.refinement_flags and _refine.ls_number_restraints.
Alias: _atom_site_restraints (cif_core.dic, 2.0.1)
Type: text
Example:
restrained to planar ring
Category: atom_site
Mandatory: no
The multiplicity of a site due to the space-group symmetry as is given in International Tables for Crystallography Vol. A (2002).
Alias: _atom_site_symmetry_multiplicity (cif_core.dic, 2.0.1)
Type: int
Range: [192, 192] [1, 192] [1, 1]
Category: atom_site
Mandatory: no
A standard code used to describe the type of atomic displacement parameters used for the site.
Alias: _atom_site_thermal_displace_type (cif_core.dic, 2.0.1)
Type: ucode
Enumeration values:
| Value | Detail |
|---|---|
Uani |
anisotropic Uij |
Uiso |
isotropic U |
Uovl |
overall U |
Umpe |
multipole expansion U |
Bani |
anisotropic Bij |
Biso |
isotropic B |
Bovl |
overall B |
Mandatory: yes
This data item is a pointer to _atom_type.symbol in the ATOM_TYPE category.
Alias: _atom_site_type_symbol (cif_core.dic, 2.0.1)
Category: atom_site
Mandatory: no
Equivalent isotropic atomic displacement parameter, Ueq, in angstroms squared, calculated as the geometric mean of the anisotropic atomic displacement parameters. Ueq = (Ui Uj Uk)1/3 Un = the principal components of the orthogonalized Uij
Alias: _atom_site_U_equiv_geom_mean (cif_core.dic, 2.0.1)
Type: float
Type conditions: esd
Units: angstroms_squared
Related items: _atom_site.U_equiv_geom_mean_esd (associated_esd) _atom_site.B_equiv_geom_mean (conversion_constant)
Range: [10.0, 10.0] [0.0, 10.0] [0.0, 0.0]
Category: atom_site
Mandatory: no
The standard uncertainty (estimated standard deviation) of _atom_site.U_equiv_geom_mean.
Type: float
Units: angstroms_squared
Related items: _atom_site.U_equiv_geom_mean (associated_value) _atom_site.B_equiv_geom_mean (conversion_constant)
Category: atom_site
Mandatory: no
Isotropic atomic displacement parameter, or equivalent isotropic atomic displacement parameter, Ueq, calculated from anisotropic atomic displacement parameters. Ueq = (1/3) sumi[sumj(Uij Ai Aj a*i a*j)] A = the real space cell lengths a* = the reciprocal space cell lengths Ref: Fischer, R. X. & Tillmanns, E. (1988). Acta Cryst. C44, 775-776.
Alias: _atom_site_U_iso_or_equiv (cif_core.dic, 2.0.1)
Type: float
Type conditions: esd
Units: angstroms_squared
Related items: _atom_site.U_iso_or_equiv_esd (associated_esd) _atom_site.B_iso_or_equiv (conversion_constant)
Range: [10.0, 10.0] [0.0, 10.0] [0.0, 0.0]
Category: atom_site
Mandatory: no
The standard uncertainty (estimated standard deviation) of _atom_site.U_iso_or_equiv.
Type: float
Units: angstroms_squared
Related items: _atom_site.U_iso_or_equiv (associated_value) _atom_site.B_iso_or_equiv_esd (conversion_constant)
Category: atom_site
Mandatory: no
The Wyckoff symbol (letter) as listed in the space-group tables of International Tables for Crystallography, Vol. A (2002).
Alias: _atom_site_Wyckoff_symbol (cif_core.dic, 2.0.1)
Type: line
Data items in the ATOM_SITE_ANISOTROP category record details about anisotropic displacement parameters. If the ATOM_SITE_ANISOTROP category is used for storing these data, the corresponding ATOM_SITE data items are not used.
Mandatory: no
Keys: _atom_site_anisotrop.id
Groups: inclusive_group atom_group
Examples:
| Example | Detail |
|---|---|
loop_
_atom_site_anisotrop.id
_atom_site_anisotrop.type_symbol
_atom_site_anisotrop.U[1][1]
_atom_site_anisotrop.U[1][2]
_atom_site_anisotrop.U[1][3]
_atom_site_anisotrop.U[2][2]
_atom_site_anisotrop.U[2][3]
_atom_site_anisotrop.U[3][3]
1 O 8642 4866 7299 -342 -258 -1427
2 C 5174 4871 6243 -1885 -2051 -1377
3 C 6202 5020 4395 -1130 -556 -632
4 O 4224 4700 5046 1105 -161 345
5 C 8684 4688 4171 -1850 -433 -292
6 O 11226 5255 3532 -341 2685 1328
7 C 10214 2428 5614 -2610 -1940 902
8 C 4590 3488 5827 751 -770 986
9 N 5014 4434 3447 -17 -1593 539
# ---- abbreviated ----
|
Example 1 - based on NDB structure BDL005 of Holbrook, Dickerson & Kim [Acta Cryst. (1985), B41, 255-262]. |
Category: atom_site_anisotrop
Mandatory: no
Sub-category: matrix
The [1][1] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sumi[sumj(Bij hi hj a*i a*j)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred.
Alias: _atom_site_aniso_B_11 (cif_core.dic, 2.0.1)
Type: float
Type conditions: esd
Units: 8pi2_angstroms_squared
Related items: _atom_site_anisotrop.B[1][1]_esd (associated_esd) _atom_site.aniso_U[1][1] (conversion_constant) _atom_site_anisotrop.U[1][1] (conversion_constant) _atom_site.aniso_B[1][1] (alternate_exclusive) _atom_site.aniso_U[1][1] (alternate_exclusive) _atom_site_anisotrop.U[1][1] (alternate_exclusive)
Category: atom_site_anisotrop
Mandatory: no
Sub-category: matrix
The standard uncertainty (estimated standard deviation) of _atom_site_anisotrop.B[1][1].
Type: float
Units: 8pi2_angstroms_squared
Related items: _atom_site_anisotrop.B[1][1] (associated_value) _atom_site.aniso_U[1][1]_esd (conversion_constant) _atom_site_anisotrop.U[1][1]_esd (conversion_constant) _atom_site.aniso_B[1][1]_esd (alternate_exclusive) _atom_site.aniso_U[1][1]_esd (alternate_exclusive) _atom_site_anisotrop.U[1][1]_esd (alternate_exclusive)
Category: atom_site_anisotrop
Mandatory: no
Sub-category: matrix
The [1][2] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sumi[sumj(Bij hi hj a*i a*j)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred.
Alias: _atom_site_aniso_B_12 (cif_core.dic, 2.0.1)
Type: float
Type conditions: esd
Units: 8pi2_angstroms_squared
Related items: _atom_site_anisotrop.B[1][2]_esd (associated_esd) _atom_site.aniso_U[1][2] (conversion_constant) _atom_site_anisotrop.U[1][2] (conversion_constant) _atom_site.aniso_B[1][2] (alternate_exclusive) _atom_site.aniso_U[1][2] (alternate_exclusive) _atom_site_anisotrop.U[1][2] (alternate_exclusive)
Category: atom_site_anisotrop
Mandatory: no
Sub-category: matrix
The standard uncertainty (estimated standard deviation) of _atom_site_anisotrop.B[1][2].
Type: float
Units: 8pi2_angstroms_squared
Related items: _atom_site_anisotrop.B[1][2] (associated_value) _atom_site.aniso_U[1][2]_esd (conversion_constant) _atom_site_anisotrop.U[1][2]_esd (conversion_constant) _atom_site.aniso_B[1][2]_esd (alternate_exclusive) _atom_site.aniso_U[1][2]_esd (alternate_exclusive) _atom_site_anisotrop.U[1][2]_esd (alternate_exclusive)
Category: atom_site_anisotrop
Mandatory: no
Sub-category: matrix
The [1][3] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sumi[sumj(Bij hi hj a*i a*j)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred.
Alias: _atom_site_aniso_B_13 (cif_core.dic, 2.0.1)
Type: float
Type conditions: esd
Units: 8pi2_angstroms_squared
Related items: _atom_site_anisotrop.B[1][3]_esd (associated_esd) _atom_site.aniso_U[1][3] (conversion_constant) _atom_site_anisotrop.U[1][3] (conversion_constant) _atom_site.aniso_B[1][3] (alternate_exclusive) _atom_site.aniso_U[1][3] (alternate_exclusive) _atom_site_anisotrop.U[1][3] (alternate_exclusive)
Category: atom_site_anisotrop
Mandatory: no
Sub-category: matrix
The standard uncertainty (estimated standard deviation) of _atom_site_anisotrop.B[1][3].
Type: float
Units: 8pi2_angstroms_squared
Related items: _atom_site_anisotrop.B[1][3] (associated_value) _atom_site.aniso_U[1][3]_esd (conversion_constant) _atom_site_anisotrop.U[1][3]_esd (conversion_constant) _atom_site.aniso_B[1][3]_esd (alternate_exclusive) _atom_site.aniso_U[1][3]_esd (alternate_exclusive) _atom_site_anisotrop.U[1][3]_esd (alternate_exclusive)
Category: atom_site_anisotrop
Mandatory: no
Sub-category: matrix
The [2][2] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sumi[sumj(Bij hi hj a*i a*j)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred.
Alias: _atom_site_aniso_B_22 (cif_core.dic, 2.0.1)
Type: float
Type conditions: esd
Units: 8pi2_angstroms_squared
Related items: _atom_site_anisotrop.B[2][2]_esd (associated_esd) _atom_site.aniso_U[2][2] (conversion_constant) _atom_site_anisotrop.U[2][2] (conversion_constant) _atom_site.aniso_B[2][2] (alternate_exclusive) _atom_site.aniso_U[2][2] (alternate_exclusive) _atom_site_anisotrop.U[2][2] (alternate_exclusive)
Category: atom_site_anisotrop
Mandatory: no
Sub-category: matrix
The standard uncertainty (estimated standard deviation) of _atom_site_anisotrop.B[2][2].
Type: float
Units: 8pi2_angstroms_squared
Related items: _atom_site_anisotrop.B[2][2] (associated_value) _atom_site.aniso_U[2][2]_esd (conversion_constant) _atom_site_anisotrop.U[2][2]_esd (conversion_constant) _atom_site.aniso_B[2][2]_esd (alternate_exclusive) _atom_site.aniso_U[2][2]_esd (alternate_exclusive) _atom_site_anisotrop.U[2][2]_esd (alternate_exclusive)
Category: atom_site_anisotrop
Mandatory: no
Sub-category: matrix
The [2][3] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sumi[sumj(Bij hi hj a*i a*j)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred.
Alias: _atom_site_aniso_B_23 (cif_core.dic, 2.0.1)
Type: float
Type conditions: esd
Units: 8pi2_angstroms_squared
Related items: _atom_site_anisotrop.B[2][3]_esd (associated_esd) _atom_site.aniso_U[2][3] (conversion_constant) _atom_site_anisotrop.U[2][3] (conversion_constant) _atom_site.aniso_B[2][3] (alternate_exclusive) _atom_site.aniso_U[2][3] (alternate_exclusive) _atom_site_anisotrop.U[2][3] (alternate_exclusive)
Category: atom_site_anisotrop
Mandatory: no
Sub-category: matrix
The standard uncertainty (estimated standard deviation) of _atom_site_anisotrop.B[2][3].
Type: float
Units: 8pi2_angstroms_squared
Related items: _atom_site_anisotrop.B[2][3] (associated_value) _atom_site.aniso_U[2][3]_esd (conversion_constant) _atom_site_anisotrop.U[2][3]_esd (conversion_constant) _atom_site.aniso_B[2][3]_esd (alternate_exclusive) _atom_site.aniso_U[2][3]_esd (alternate_exclusive) _atom_site_anisotrop.U[2][3]_esd (alternate_exclusive)
Category: atom_site_anisotrop
Mandatory: no
Sub-category: matrix
The [3][3] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sumi[sumj(Bij hi hj a*i a*j)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred.
Alias: _atom_site_aniso_B_33 (cif_core.dic, 2.0.1)
Type: float
Type conditions: esd
Units: 8pi2_angstroms_squared
Related items: _atom_site_anisotrop.B[3][3]_esd (associated_esd) _atom_site.aniso_U[3][3] (conversion_constant) _atom_site_anisotrop.U[3][3] (conversion_constant) _atom_site.aniso_B[3][3] (alternate_exclusive) _atom_site.aniso_U[3][3] (alternate_exclusive) _atom_site_anisotrop.U[3][3] (alternate_exclusive)
Category: atom_site_anisotrop
Mandatory: no
Sub-category: matrix
The standard uncertainty (estimated standard deviation) of _atom_site_anisotrop.B[3][3].
Type: float
Units: 8pi2_angstroms_squared
Related items: _atom_site_anisotrop.B[3][3] (associated_value) _atom_site.aniso_U[3][3]_esd (conversion_constant) _atom_site_anisotrop.U[3][3]_esd (conversion_constant) _atom_site.aniso_B[3][3]_esd (alternate_exclusive) _atom_site.aniso_U[3][3]_esd (alternate_exclusive) _atom_site_anisotrop.U[3][3]_esd (alternate_exclusive)
Category: atom_site_anisotrop
Mandatory: no
Ratio of the maximum to minimum principal axes of displacement (thermal) ellipsoids.
Alias: _atom_site_aniso_ratio (cif_core.dic, 2.0.1)
Type: float
Related item: _atom_site.aniso_ratio (alternate_exclusive)
Range: [1.0, .] [1.0, 1.0]
Mandatory: yes
This data item is a pointer to _atom_site.id in the ATOM_SITE category.
Alias: _atom_site_aniso_label (cif_core.dic, 2.0.1)
Mandatory: yes
This data item is a pointer to _atom_type.symbol in the ATOM_TYPE category.
Alias: _atom_site_aniso_type_symbol (cif_core.dic, 2.0.1)
Category: atom_site_anisotrop
Mandatory: no
Sub-category: matrix
The [1][1] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi2 sumi[sumj(Uij hi hj a*i a*j)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row.
Alias: _atom_site_aniso_U_11 (cif_core.dic, 2.0.1)
Type: float
Type conditions: esd
Units: angstroms_squared
Related items: _atom_site_anisotrop.U[1][1]_esd (associated_esd) _atom_site.aniso_B[1][1] (conversion_constant) _atom_site_anisotrop.B[1][1] (conversion_constant) _atom_site.aniso_B[1][1] (alternate_exclusive) _atom_site.aniso_U[1][1] (alternate_exclusive) _atom_site_anisotrop.B[1][1] (alternate_exclusive)
Category: atom_site_anisotrop
Mandatory: no
Sub-category: matrix
The standard uncertainty (estimated standard deviation) of _atom_site_anisotrop.U[1][1].
Type: float
Units: angstroms_squared
Related items: _atom_site_anisotrop.U[1][1] (associated_value) _atom_site.aniso_B[1][1]_esd (conversion_constant) _atom_site_anisotrop.B[1][1]_esd (conversion_constant) _atom_site.aniso_B[1][1]_esd (alternate_exclusive) _atom_site.aniso_U[1][1]_esd (alternate_exclusive) _atom_site_anisotrop.B[1][1]_esd (alternate_exclusive)
Category: atom_site_anisotrop
Mandatory: no
Sub-category: matrix
The [1][2] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi2 sumi[sumj(Uij hi hj a*i a*j)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row.
Alias: _atom_site_aniso_U_12 (cif_core.dic, 2.0.1)
Type: float
Type conditions: esd
Units: angstroms_squared
Related items: _atom_site_anisotrop.U[1][2]_esd (associated_esd) _atom_site.aniso_B[1][2] (conversion_constant) _atom_site_anisotrop.B[1][2] (conversion_constant) _atom_site.aniso_B[1][2] (alternate_exclusive) _atom_site.aniso_U[1][2] (alternate_exclusive) _atom_site_anisotrop.B[1][2] (alternate_exclusive)
Category: atom_site_anisotrop
Mandatory: no
Sub-category: matrix
The standard uncertainty (estimated standard deviation) of _atom_site_anisotrop.U[1][2].
Type: float
Units: angstroms_squared
Related items: _atom_site_anisotrop.U[1][2] (associated_value) _atom_site.aniso_B[1][2]_esd (conversion_constant) _atom_site_anisotrop.B[1][2]_esd (conversion_constant) _atom_site.aniso_B[1][2]_esd (alternate_exclusive) _atom_site.aniso_U[1][2]_esd (alternate_exclusive) _atom_site_anisotrop.B[1][2]_esd (alternate_exclusive)
Category: atom_site_anisotrop
Mandatory: no
Sub-category: matrix
The [1][3] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi2 sumi[sumj(Uij hi hj a*i a*j)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row.
Alias: _atom_site_aniso_U_13 (cif_core.dic, 2.0.1)
Type: float
Type conditions: esd
Units: angstroms_squared
Related items: _atom_site_anisotrop.U[1][3]_esd (associated_esd) _atom_site.aniso_B[1][3] (conversion_constant) _atom_site_anisotrop.B[1][3] (conversion_constant) _atom_site.aniso_B[1][3] (alternate_exclusive) _atom_site.aniso_U[1][3] (alternate_exclusive) _atom_site_anisotrop.B[1][3] (alternate_exclusive)
Category: atom_site_anisotrop
Mandatory: no
Sub-category: matrix
The standard uncertainty (estimated standard deviation) of _atom_site_anisotrop.U[1][3].
Type: float
Units: angstroms_squared
Related items: _atom_site_anisotrop.U[1][3] (associated_value) _atom_site.aniso_B[1][3]_esd (conversion_constant) _atom_site_anisotrop.B[1][3]_esd (conversion_constant) _atom_site.aniso_B[1][3]_esd (alternate_exclusive) _atom_site.aniso_U[1][3]_esd (alternate_exclusive) _atom_site_anisotrop.B[1][3]_esd (alternate_exclusive)
Category: atom_site_anisotrop
Mandatory: no
Sub-category: matrix
The [2][2] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi2 sumi[sumj(Uij hi hj a*i a*j)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row.
Alias: _atom_site_aniso_U_22 (cif_core.dic, 2.0.1)
Type: float
Type conditions: esd
Units: angstroms_squared
Related items: _atom_site_anisotrop.U[2][2]_esd (associated_esd) _atom_site.aniso_B[2][2] (conversion_constant) _atom_site_anisotrop.B[2][2] (conversion_constant) _atom_site.aniso_B[2][2] (alternate_exclusive) _atom_site.aniso_U[2][2] (alternate_exclusive) _atom_site_anisotrop.B[2][2] (alternate_exclusive)
Category: atom_site_anisotrop
Mandatory: no
Sub-category: matrix
The standard uncertainty (estimated standard deviation) of _atom_site_anisotrop.U[2][2].
Type: float
Units: angstroms_squared
Related items: _atom_site_anisotrop.U[2][2] (associated_value) _atom_site.aniso_B[2][2]_esd (conversion_constant) _atom_site_anisotrop.B[2][2]_esd (conversion_constant) _atom_site.aniso_B[2][2]_esd (alternate_exclusive) _atom_site.aniso_U[2][2]_esd (alternate_exclusive) _atom_site_anisotrop.B[2][2]_esd (alternate_exclusive)
Category: atom_site_anisotrop
Mandatory: no
Sub-category: matrix
The [2][3] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi2 sumi[sumj(Uij hi hj a*i a*j)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row.
Alias: _atom_site_aniso_U_23 (cif_core.dic, 2.0.1)
Type: float
Type conditions: esd
Units: angstroms_squared
Related items: _atom_site_anisotrop.U[2][3]_esd (associated_esd) _atom_site.aniso_B[2][3] (conversion_constant) _atom_site_anisotrop.B[2][3] (conversion_constant) _atom_site.aniso_B[2][3] (alternate_exclusive) _atom_site.aniso_U[2][3] (alternate_exclusive) _atom_site_anisotrop.B[2][3] (alternate_exclusive)
Category: atom_site_anisotrop
Mandatory: no
Sub-category: matrix
The standard uncertainty (estimated standard deviation) of _atom_site_anisotrop.U[2][3].
Type: float
Units: angstroms_squared
Related items: _atom_site_anisotrop.U[2][3] (associated_value) _atom_site.aniso_B[2][3]_esd (conversion_constant) _atom_site_anisotrop.B[2][3]_esd (conversion_constant) _atom_site.aniso_B[2][3]_esd (alternate_exclusive) _atom_site.aniso_U[2][3]_esd (alternate_exclusive) _atom_site_anisotrop.B[2][3]_esd (alternate_exclusive)
Category: atom_site_anisotrop
Mandatory: no
Sub-category: matrix
The [3][3] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi2 sumi[sumj(Uij hi hj a*i a*j)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row.
Alias: _atom_site_aniso_U_33 (cif_core.dic, 2.0.1)
Type: float
Type conditions: esd
Units: angstroms_squared
Related items: _atom_site_anisotrop.U[3][3]_esd (associated_esd) _atom_site.aniso_B[3][3] (conversion_constant) _atom_site_anisotrop.B[3][3] (conversion_constant) _atom_site.aniso_B[3][3] (alternate_exclusive) _atom_site.aniso_U[3][3] (alternate_exclusive) _atom_site_anisotrop.B[3][3] (alternate_exclusive)
Category: atom_site_anisotrop
Mandatory: no
The standard uncertainty (estimated standard deviation) of _atom_site_anisotrop.U[3][3].
Type: float
Units: angstroms_squared
Related items: _atom_site_anisotrop.U[3][3] (associated_value) _atom_site.aniso_B[3][3]_esd (conversion_constant) _atom_site_anisotrop.B[3][3]_esd (conversion_constant) _atom_site.aniso_B[3][3]_esd (alternate_exclusive) _atom_site.aniso_U[3][3]_esd (alternate_exclusive) _atom_site_anisotrop.B[3][3]_esd (alternate_exclusive)
Data items in the ATOM_SITES category record details about the crystallographic cell and cell transformations, which are common to all atom sites.
Mandatory: no
Keys: _atom_sites.entry_id
Groups: inclusive_group atom_group
Examples:
| Example | Detail |
|---|---|
_atom_sites.entry_id '5HVP'
_atom_sites.Cartn_transform_axes
'c along z, astar along x, b along y'
_atom_sites.Cartn_transf_matrix[1][1] 58.39
_atom_sites.Cartn_transf_matrix[1][2] 0.00
_atom_sites.Cartn_transf_matrix[1][3] 0.00
_atom_sites.Cartn_transf_matrix[2][1] 0.00
_atom_sites.Cartn_transf_matrix[2][2] 86.70
_atom_sites.Cartn_transf_matrix[2][3] 0.00
_atom_sites.Cartn_transf_matrix[3][1] 0.00
_atom_sites.Cartn_transf_matrix[3][2] 0.00
_atom_sites.Cartn_transf_matrix[3][3] 46.27
_atom_sites.Cartn_transf_vector[1] 0.00
_atom_sites.Cartn_transf_vector[2] 0.00
_atom_sites.Cartn_transf_vector[3] 0.00
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
Mandatory: yes
This data item is a pointer to _entry.id in the ENTRY category.
Category: atom_sites
Mandatory: no
Sub-category: matrix
The [1][1] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.Cartn_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|Cartesian = |21 22 23| |y|fractional + |2| |z'| |31 32 33| |z| |3|
Alias: _atom_sites_Cartn_tran_matrix_11 (cif_core.dic, 2.0.1)
Type: float
Category: atom_sites
Mandatory: no
Sub-category: matrix
The [1][2] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.Cartn_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|Cartesian = |21 22 23| |y|fractional + |2| |z'| |31 32 33| |z| |3|
Alias: _atom_sites_Cartn_tran_matrix_12 (cif_core.dic, 2.0.1)
Type: float
Category: atom_sites
Mandatory: no
Sub-category: matrix
The [1][3] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.Cartn_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|Cartesian = |21 22 23| |y|fractional + |2| |z'| |31 32 33| |z| |3|
Alias: _atom_sites_Cartn_tran_matrix_13 (cif_core.dic, 2.0.1)
Type: float
Category: atom_sites
Mandatory: no
Sub-category: matrix
The [2][1] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.Cartn_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|Cartesian = |21 22 23| |y|fractional + |2| |z'| |31 32 33| |z| |3|
Alias: _atom_sites_Cartn_tran_matrix_21 (cif_core.dic, 2.0.1)
Type: float
Category: atom_sites
Mandatory: no
Sub-category: matrix
The [2][2] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.Cartn_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|Cartesian = |21 22 23| |y|fractional + |2| |z'| |31 32 33| |z| |3|
Alias: _atom_sites_Cartn_tran_matrix_22 (cif_core.dic, 2.0.1)
Type: float
Category: atom_sites
Mandatory: no
Sub-category: matrix
The [2][3] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.Cartn_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|Cartesian = |21 22 23| |y|fractional + |2| |z'| |31 32 33| |z| |3|
Alias: _atom_sites_Cartn_tran_matrix_23 (cif_core.dic, 2.0.1)
Type: float
Category: atom_sites
Mandatory: no
Sub-category: matrix
The [3][1] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.Cartn_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|Cartesian = |21 22 23| |y|fractional + |2| |z'| |31 32 33| |z| |3|
Alias: _atom_sites_Cartn_tran_matrix_31 (cif_core.dic, 2.0.1)
Type: float
Category: atom_sites
Mandatory: no
Sub-category: matrix
The [3][2] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.Cartn_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|Cartesian = |21 22 23| |y|fractional + |2| |z'| |31 32 33| |z| |3|
Alias: _atom_sites_Cartn_tran_matrix_32 (cif_core.dic, 2.0.1)
Type: float
Category: atom_sites
Mandatory: no
Sub-category: matrix
The [3][3] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.Cartn_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|Cartesian = |21 22 23| |y|fractional + |2| |z'| |31 32 33| |z| |3|
Alias: _atom_sites_Cartn_tran_matrix_33 (cif_core.dic, 2.0.1)
Type: float
Category: atom_sites
Mandatory: no
Sub-category: vector
The [1] element of the three-element vector used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The rotation matrix is defined in _atom_sites.Cartn_transf_matrix[][]. |x'| |11 12 13| |x| |1| |y'|Cartesian = |21 22 23| |y|fractional + |2| |z'| |31 32 33| |z| |3|
Alias: _atom_sites_Cartn_tran_vector_1 (cif_core.dic, 2.0.1)
Type: float
Category: atom_sites
Mandatory: no
Sub-category: vector
The [2] element of the three-element vector used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The rotation matrix is defined in _atom_sites.Cartn_transf_matrix[][]. |x'| |11 12 13| |x| |1| |y'|Cartesian = |21 22 23| |y|fractional + |2| |z'| |31 32 33| |z| |3|
Alias: _atom_sites_Cartn_tran_vector_2 (cif_core.dic, 2.0.1)
Type: float
Category: atom_sites
Mandatory: no
Sub-category: vector
The [3] element of the three-element vector used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The rotation matrix is defined in _atom_sites.Cartn_transf_matrix[][]. |x'| |11 12 13| |x| |1| |y'|Cartesian = |21 22 23| |y|fractional + |2| |z'| |31 32 33| |z| |3|
Alias: _atom_sites_Cartn_tran_vector_3 (cif_core.dic, 2.0.1)
Type: float
Category: atom_sites
Mandatory: no
A description of the relative alignment of the crystal cell axes to the Cartesian orthogonal axes as applied in the transformation matrix _atom_sites.Cartn_transf_matrix[][].
Alias: _atom_sites_Cartn_transform_axes (cif_core.dic, 2.0.1)
Type: text
Example:
a parallel to x; b in the plane of y and z
Category: atom_sites
Mandatory: no
Sub-category: matrix
The [1][1] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.fract_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|fractional = |21 22 23| |y|Cartesian + |2| |z'| |31 32 33| |z| |3|
Alias: _atom_sites_fract_tran_matrix_11 (cif_core.dic, 2.0.1)
Type: float
Category: atom_sites
Mandatory: no
Sub-category: matrix
The [1][2] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.fract_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|fractional = |21 22 23| |y|Cartesian + |2| |z'| |31 32 33| |z| |3|
Alias: _atom_sites_fract_tran_matrix_12 (cif_core.dic, 2.0.1)
Type: float
Category: atom_sites
Mandatory: no
Sub-category: matrix
The [1][3] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.fract_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|fractional = |21 22 23| |y|Cartesian + |2| |z'| |31 32 33| |z| |3|
Alias: _atom_sites_fract_tran_matrix_13 (cif_core.dic, 2.0.1)
Type: float
Category: atom_sites
Mandatory: no
Sub-category: matrix
The [2][1] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.fract_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|fractional = |21 22 23| |y|Cartesian + |2| |z'| |31 32 33| |z| |3|
Alias: _atom_sites_fract_tran_matrix_21 (cif_core.dic, 2.0.1)
Type: float
Category: atom_sites
Mandatory: no
Sub-category: matrix
The [2][2] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.fract_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|fractional = |21 22 23| |y|Cartesian + |2| |z'| |31 32 33| |z| |3|
Alias: _atom_sites_fract_tran_matrix_22 (cif_core.dic, 2.0.1)
Type: float
Category: atom_sites
Mandatory: no
Sub-category: matrix
The [2][3] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.fract_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|fractional = |21 22 23| |y|Cartesian + |2| |z'| |31 32 33| |z| |3|
Alias: _atom_sites_fract_tran_matrix_23 (cif_core.dic, 2.0.1)
Type: float
Category: atom_sites
Mandatory: no
Sub-category: matrix
The [3][1] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.fract_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|fractional = |21 22 23| |y|Cartesian + |2| |z'| |31 32 33| |z| |3|
Alias: _atom_sites_fract_tran_matrix_31 (cif_core.dic, 2.0.1)
Type: float
Category: atom_sites
Mandatory: no
Sub-category: matrix
The [3][2] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.fract_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|fractional = |21 22 23| |y|Cartesian + |2| |z'| |31 32 33| |z| |3|
Alias: _atom_sites_fract_tran_matrix_32 (cif_core.dic, 2.0.1)
Type: float
Category: atom_sites
Mandatory: no
Sub-category: matrix
The [3][3] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x1 translation is defined in _atom_sites.fract_transf_vector[]. |x'| |11 12 13| |x| |1| |y'|fractional = |21 22 23| |y|Cartesian + |2| |z'| |31 32 33| |z| |3|
Alias: _atom_sites_fract_tran_matrix_33 (cif_core.dic, 2.0.1)
Type: float
Category: atom_sites
Mandatory: no
Sub-category: vector
The [1] element of the three-element vector used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x3 rotation is defined in _atom_sites.fract_transf_matrix[][]. |x'| |11 12 13| |x| |1| |y'|fractional = |21 22 23| |y|Cartesian + |2| |z'| |31 32 33| |z| |3|
Alias: _atom_sites_fract_tran_vector_1 (cif_core.dic, 2.0.1)
Type: float
Category: atom_sites
Mandatory: no
Sub-category: vector
The [2] element of the three-element vector used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x3 rotation is defined in _atom_sites.fract_transf_matrix[][]. |x'| |11 12 13| |x| |1| |y'|fractional = |21 22 23| |y|Cartesian + |2| |z'| |31 32 33| |z| |3|
Alias: _atom_sites_fract_tran_vector_2 (cif_core.dic, 2.0.1)
Type: float
Category: atom_sites
Mandatory: no
Sub-category: vector
The [3] element of the three-element vector used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in _atom_sites.Cartn_transform_axes. The 3x3 rotation is defined in _atom_sites.fract_transf_matrix[][]. |x'| |11 12 13| |x| |1| |y'|fractional = |21 22 23| |y|Cartesian + |2| |z'| |31 32 33| |z| |3|
Alias: _atom_sites_fract_tran_vector_3 (cif_core.dic, 2.0.1)
Type: float
Category: atom_sites
Mandatory: no
This code identifies the method used to locate the initial atom sites. *** This data item would not in general be used in a macromolecular data block. ***
Alias: _atom_sites_solution_primary (cif_core.dic, 2.0.1)
Type: ucode
Enumeration values:
| Value | Detail |
|---|---|
difmap |
difference Fourier map |
vecmap |
real-space vector search |
heavy |
heavy-atom method |
direct |
structure-invariant direct methods |
geom |
inferred from neighbouring sites |
disper |
anomalous-dispersion techniques |
isomor |
isomorphous structure methods |
Category: atom_sites
Mandatory: no
This code identifies the method used to locate the non-hydrogen-atom sites not found by _atom_sites.solution_primary. *** This data item would not in general be used in a macromolecular data block. ***
Alias: _atom_sites_solution_secondary (cif_core.dic, 2.0.1)
Type: ucode
Enumeration values:
| Value | Detail |
|---|---|
difmap |
difference Fourier map |
vecmap |
real-space vector search |
heavy |
heavy-atom method |
direct |
structure-invariant direct methods |
geom |
inferred from neighbouring sites |
disper |
anomalous-dispersion techniques |
isomor |
isomorphous structure methods |
Category: atom_sites
Mandatory: no
This code identifies the method used to locate the hydrogen atoms. *** This data item would not in general be used in a macromolecular data block. ***
Alias: _atom_sites_solution_hydrogens (cif_core.dic, 2.0.1)
Type: ucode
Enumeration values:
| Value | Detail |
|---|---|
difmap |
difference Fourier map |
vecmap |
real-space vector search |
heavy |
heavy-atom method |
direct |
structure-invariant direct methods |
geom |
inferred from neighbouring sites |
disper |
anomalous-dispersion techniques |
isomor |
isomorphous structure methods |
Data items in the ATOM_SITES_ALT category record details about the structural ensembles that should be generated from atom sites or groups of atom sites that are modelled in alternative conformations in this data block.
Mandatory: no
Keys: _atom_sites_alt.id
Groups: inclusive_group atom_group
Examples:
| Example | Detail |
|---|---|
loop_
_atom_sites_alt.id
_atom_sites_alt.details
.
; Atom sites with the alternative ID set to null are not
modeled in alternative conformations
;
1
; Atom sites with the alternative ID set to 1 have been
modeled in alternative conformations with respect to atom
sites marked with alternative ID 2. The conformations of
amino-acid side chains and solvent atoms with alternative
ID set to 1 correlate with the conformation of the
inhibitor marked with alternative ID 1. They have been
given an occupancy of 0.58 to match the occupancy assigned
to the inhibitor.
;
2
; Atom sites with the alternative ID set to 2 have been
modeled in alternative conformations with respect to atom
sites marked with alternative ID 1. The conformations of
amino-acid side chains and solvent atoms with alternative
ID set to 2 correlate with the conformation of the
inhibitor marked with alternative ID 2. They have been
given an occupancy of 0.42 to match the occupancy assigned
to the inhibitor.
;
3
; Atom sites with the alternative ID set to 3 have been
modeled in alternative conformations with respect to
atoms marked with alternative ID 4. The conformations of
amino-acid side chains and solvent atoms with alternative
ID set to 3 do not correlate with the conformation of the
inhibitor. These atom sites have arbitrarily been given
an occupancy of 0.50.
;
4
; Atom sites with the alternative ID set to 4 have been
modeled in alternative conformations with respect to
atoms marked with alternative ID 3. The conformations of
amino-acid side chains and solvent atoms with alternative
ID set to 4 do not correlate with the conformation of the
inhibitor. These atom sites have arbitrarily been given
an occupancy of 0.50.
;
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
Category: atom_sites_alt
Mandatory: no
A description of special aspects of the modelling of atoms in alternative conformations.
Type: text
| Name | Category | Mandatory |
|---|---|---|
| _atom_sites_alt.id | atom_sites_alt | yes |
| _atom_site.label_alt_id | atom_site | no |
| _atom_sites_alt_gen.alt_id | atom_sites_alt_gen | yes |
| _geom_angle.atom_site_label_alt_id_1 | geom_angle | no |
| _geom_angle.atom_site_label_alt_id_2 | geom_angle | no |
| _geom_angle.atom_site_label_alt_id_3 | geom_angle | no |
| _geom_bond.atom_site_label_alt_id_1 | geom_bond | no |
| _geom_bond.atom_site_label_alt_id_2 | geom_bond | no |
| _geom_contact.atom_site_label_alt_id_1 | geom_contact | no |
| _geom_contact.atom_site_label_alt_id_2 | geom_contact | no |
| _geom_hbond.atom_site_label_alt_id_A | geom_hbond | no |
| _geom_hbond.atom_site_label_alt_id_D | geom_hbond | no |
| _geom_hbond.atom_site_label_alt_id_H | geom_hbond | no |
| _geom_torsion.atom_site_label_alt_id_1 | geom_torsion | no |
| _geom_torsion.atom_site_label_alt_id_2 | geom_torsion | no |
| _geom_torsion.atom_site_label_alt_id_3 | geom_torsion | no |
| _geom_torsion.atom_site_label_alt_id_4 | geom_torsion | no |
| _struct_conn.ptnr1_label_alt_id | struct_conn | no |
| _struct_conn.ptnr2_label_alt_id | struct_conn | no |
| _struct_mon_nucl.label_alt_id | struct_mon_nucl | yes |
| _struct_mon_prot.label_alt_id | struct_mon_prot | yes |
| _struct_mon_prot_cis.label_alt_id | struct_mon_prot_cis | yes |
| _struct_ncs_dom_lim.beg_label_alt_id | struct_ncs_dom_lim | yes |
| _struct_ncs_dom_lim.end_label_alt_id | struct_ncs_dom_lim | yes |
| _struct_site_gen.label_alt_id | struct_site_gen | yes |
The value of _atom_sites_alt.id must uniquely identify a record in the ATOM_SITES_ALT list. Note that this item need not be a number; it can be any unique identifier.
Type: code
Child / Parent relations:
Examples:
| Example | Detail |
|---|---|
orientation 1 |
|
molecule abc |
Data items in the ATOM_SITES_ALT_ENS category record details about the ensemble structure generated from atoms with various alternative conformation IDs.
Mandatory: no
Keys: _atom_sites_alt_ens.id
Groups: inclusive_group atom_group
Examples:
| Example | Detail |
|---|---|
loop_
_atom_sites_alt_ens.id
_atom_sites_alt_ens.details
'Ensemble 1-A'
; The inhibitor binds to the enzyme in two, roughly twofold
symmetric alternative conformations.
This conformational ensemble includes the more populated
conformation of the inhibitor (ID=1) and the amino-acid
side chains and solvent structure that correlate with this
inhibitor conformation.
Also included are one set (ID=3) of side chains with
alternative conformations when the conformations are not
correlated with the inhibitor conformation.
;
'Ensemble 1-B'
; The inhibitor binds to the enzyme in two, roughly twofold
symmetric alternative conformations.
This conformational ensemble includes the more populated
conformation of the inhibitor (ID=1) and the amino-acid
side chains and solvent structure that correlate with
this inhibitor conformation.
Also included are one set (ID=4) of side chains with
alternative conformations when the conformations are not
correlated with the inhibitor conformation.
;
'Ensemble 2-A'
; The inhibitor binds to the enzyme in two, roughly twofold
symmetric alternative conformations.
This conformational ensemble includes the less populated
conformation of the inhibitor (ID=2) and the amino-acid
side chains and solvent structure that correlate with this
inhibitor conformation.
Also included are one set (ID=3) of side chains with
alternative conformations when the conformations are not
correlated with the inhibitor conformation.
;
'Ensemble 2-B'
; The inhibitor binds to the enzyme in two, roughly twofold
symmetric alternative conformations.
This conformational ensemble includes the less populated
conformation of the inhibitor (ID=2) and the amino-acid
side chains and solvent structure that correlate with this
inhibitor conformation.
Also included are one set (ID=4) of side chains with
alternative conformations when the conformations are not
correlated with the inhibitor conformation.
;
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
Category: atom_sites_alt_ens
Mandatory: no
A description of special aspects of the ensemble structure generated from atoms with various alternative IDs.
Type: text
| Name | Category | Mandatory |
|---|---|---|
| _atom_sites_alt_ens.id | atom_sites_alt_ens | yes |
| _atom_sites_alt_gen.ens_id | atom_sites_alt_gen | yes |
The value of _atom_sites_alt_ens.id must uniquely identify a record in the ATOM_SITES_ALT_ENS list. Note that this item need not be a number; it can be any unique identifier.
Type: code
Child / Parent relations:
| Child | Parent |
|---|---|
| _atom_sites_alt_gen.ens_id | _atom_sites_alt_ens.id |
Data items in the ATOM_SITES_ALT_GEN category record details about the interpretation of multiple conformations in the structure.
Mandatory: no
Keys: _atom_sites_alt_gen.ens_id _atom_sites_alt_gen.alt_id
Groups: inclusive_group atom_group
Examples:
| Example | Detail |
|---|---|
loop_
_atom_sites_alt_gen.ens_id
_atom_sites_alt_gen.alt_id
'Ensemble 1-A' .
'Ensemble 1-A' 1
'Ensemble 1-A' 3
'Ensemble 1-B' .
'Ensemble 1-B' 1
'Ensemble 1-B' 4
'Ensemble 2-A' .
'Ensemble 2-A' 2
'Ensemble 2-A' 3
'Ensemble 2-B' .
'Ensemble 2-B' 2
'Ensemble 2-B' 4
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
Mandatory: yes
This data item is a pointer to _atom_sites_alt.id in the ATOM_SITES_ALT category.
Mandatory: yes
This data item is a pointer to _atom_sites_alt_ens.id in the ATOM_SITES_ALT_ENS category.
Data items in the ATOM_SITES_FOOTNOTE category record detailed comments about an atom site or a group of atom sites.
Mandatory: no
Keys: _atom_sites_footnote.id
Groups: inclusive_group atom_group
Examples:
| Example | Detail |
|---|---|
loop_
_atom_sites_footnote.id
_atom_sites_footnote.text
1
; The inhibitor binds to the enzyme in two alternative
orientations. The two orientations have been assigned
alternative IDs *1* and *2*.
;
2
; Side chains of these residues adopt alternative
orientations that correlate with the alternative
orientations of the inhibitor.
Side chains with alternative ID *1* and occupancy 0.58
correlate with inhibitor orientation *1*.
Side chains with alternative ID *2* and occupancy 0.42
correlate with inhibitor orientation *2*.
;
3
; The positions of these water molecules correlate with
the alternative orientations of the inhibitor.
Water molecules with alternative ID *1* and occupancy 0.58
correlate with inhibitor orientation *1*.
Water molecules with alternative ID *2* and occupancy 0.42
correlate with inhibitor orientation *2*.
;
4
; Side chains of these residues adopt alternative
orientations that do not correlate with the alternative
orientation of the inhibitor.
;
5
; The positions of these water molecules correlate with
alternative orientations of amino-acid side chains that
do not correlate with alternative orientations of the
inhibitor.
;
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
| Name | Category | Mandatory |
|---|---|---|
| _atom_sites_footnote.id | atom_sites_footnote | yes |
| _atom_site.footnote_id | atom_site | no |
A code that identifies the footnote.
Type: code
Child / Parent relations:
| Child | Parent |
|---|---|
| _atom_site.footnote_id | _atom_sites_footnote.id |
Examples:
| Example | Detail |
|---|---|
a |
|
b |
|
1 |
|
2 |
Category: atom_sites_footnote
Mandatory: no
The text of the footnote. Footnotes are used to describe an atom site or a group of atom sites in the ATOM_SITE list. For example, footnotes may be used to indicate atoms for which the electron density is very weak, or atoms for which static disorder has been modelled.
Type: text
Data items in the ATOM_TYPE category record details about the properties of the atoms that occupy the atom sites, such as the atomic scattering factors.
Mandatory: no
Keys: _atom_type.symbol
Groups: inclusive_group atom_group
Examples:
| Example | Detail |
|---|---|
loop_
_atom_type.symbol
_atom_type.oxidation_number
_atom_type.scat_Cromer_Mann_a1
_atom_type.scat_Cromer_Mann_a2
_atom_type.scat_Cromer_Mann_a3
_atom_type.scat_Cromer_Mann_a4
_atom_type.scat_Cromer_Mann_b1
_atom_type.scat_Cromer_Mann_b2
_atom_type.scat_Cromer_Mann_b3
_atom_type.scat_Cromer_Mann_b4
_atom_type.scat_Cromer_Mann_c
C 0 2.31000 20.8439 1.02000 10.2075
1.58860 0.568700 0.865000 51.6512 0.21560
N 0 12.2126 0.005700 3.13220 9.89330
2.01250 28.9975 1.16630 0.582600 -11.529
O 0 3.04850 13.2771 2.28680 5.70110
1.54630 0.323900 0.867000 32.9089 0.250800
S 0 6.90530 1.46790 5.20340 22.2151
1.43790 0.253600 1.58630 56.1720 0.866900
CL -1 18.2915 0.006600 7.20840 1.17170
6.53370 19.5424 2.33860 60.4486 -16.378
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
loop_
_atom_type.symbol
_atom_type.oxidation_number
_atom_type.number_in_cell
_atom_type.scat_dispersion_real
_atom_type.scat_dispersion_imag
_atom_type.scat_source
C 0 72 .017 .009 International_Tables_Vol_IV_Table_2.2B
H 0 100 0 0 International_Tables_Vol_IV_Table_2.2B
O 0 12 .047 .032 International_Tables_Vol_IV_Table_2.2B
N 0 4 .029 .018 International_Tables_Vol_IV_Table_2.2B
|
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. |
Category: atom_type
Mandatory: no
Mass percentage of this atom type derived from chemical analysis.
Alias: _atom_type_analytical_mass_% (cif_core.dic, 2.0.1)
Type: float
Range: [0.0, .] [0.0, 0.0]
Category: atom_type
Mandatory: no
A description of the atom(s) designated by this atom type. In most cases, this is the element name and oxidation state of a single atom species. For disordered or nonstoichiometric structures it will describe a combination of atom species.
Alias: _atom_type_description (cif_core.dic, 2.0.1)
Type: text
Examples:
| Example | Detail |
|---|---|
deuterium |
|
0.34Fe+0.66Ni |
Category: atom_type
Mandatory: no
Total number of atoms of this atom type in the unit cell.
Alias: _atom_type_number_in_cell (cif_core.dic, 2.0.1)
Type: int
Range: [0, .] [0, 0]
Category: atom_type
Mandatory: no
Formal oxidation state of this atom type in the structure.
Alias: _atom_type_oxidation_number (cif_core.dic, 2.0.1)
Type: int
Default value: 0
Range: [8, 8] [-8, 8] [-8, -8]
Category: atom_type
Mandatory: no
The effective intramolecular bonding radius in angstroms of this atom type.
Alias: _atom_type_radius_bond (cif_core.dic, 2.0.1)
Type: float
Units: angstroms
Range: [5.0, 5.0] [0.0, 5.0] [0.0, 0.0]
Category: atom_type
Mandatory: no
The effective intermolecular bonding radius in angstroms of this atom type.
Alias: _atom_type_radius_contact (cif_core.dic, 2.0.1)
Type: float
Units: angstroms
Range: [5.0, 5.0] [0.0, 5.0] [0.0, 0.0]
Category: atom_type
Mandatory: no
The Cromer-Mann scattering-factor coefficient a1 used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5.
Alias: _atom_type_scat_Cromer_Mann_a1 (cif_core.dic, 2.0.1)
Type: float
Dependent items: _atom_type.scat_Cromer_Mann_a2 _atom_type.scat_Cromer_Mann_a3 _atom_type.scat_Cromer_Mann_a4 _atom_type.scat_Cromer_Mann_b1 _atom_type.scat_Cromer_Mann_b2 _atom_type.scat_Cromer_Mann_b3 _atom_type.scat_Cromer_Mann_b4 _atom_type.scat_Cromer_Mann_c
Category: atom_type
Mandatory: no
The Cromer-Mann scattering-factor coefficient a2 used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5.
Alias: _atom_type_scat_Cromer_Mann_a2 (cif_core.dic, 2.0.1)
Type: float
Dependent items: _atom_type.scat_Cromer_Mann_a1 _atom_type.scat_Cromer_Mann_a3 _atom_type.scat_Cromer_Mann_a4 _atom_type.scat_Cromer_Mann_b1 _atom_type.scat_Cromer_Mann_b2 _atom_type.scat_Cromer_Mann_b3 _atom_type.scat_Cromer_Mann_b4 _atom_type.scat_Cromer_Mann_c
Category: atom_type
Mandatory: no
The Cromer-Mann scattering-factor coefficient a3 used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5.
Alias: _atom_type_scat_Cromer_Mann_a3 (cif_core.dic, 2.0.1)
Type: float
Dependent items: _atom_type.scat_Cromer_Mann_a1 _atom_type.scat_Cromer_Mann_a2 _atom_type.scat_Cromer_Mann_a4 _atom_type.scat_Cromer_Mann_b1 _atom_type.scat_Cromer_Mann_b2 _atom_type.scat_Cromer_Mann_b3 _atom_type.scat_Cromer_Mann_b4 _atom_type.scat_Cromer_Mann_c
Category: atom_type
Mandatory: no
The Cromer-Mann scattering-factor coefficient a4 used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5.
Alias: _atom_type_scat_Cromer_Mann_a4 (cif_core.dic, 2.0.1)
Type: float
Dependent items: _atom_type.scat_Cromer_Mann_a1 _atom_type.scat_Cromer_Mann_a2 _atom_type.scat_Cromer_Mann_a3 _atom_type.scat_Cromer_Mann_b1 _atom_type.scat_Cromer_Mann_b2 _atom_type.scat_Cromer_Mann_b3 _atom_type.scat_Cromer_Mann_b4 _atom_type.scat_Cromer_Mann_c
Category: atom_type
Mandatory: no
The Cromer-Mann scattering-factor coefficient b1 used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5.
Alias: _atom_type_scat_Cromer_Mann_b1 (cif_core.dic, 2.0.1)
Type: float
Dependent items: _atom_type.scat_Cromer_Mann_a1 _atom_type.scat_Cromer_Mann_a2 _atom_type.scat_Cromer_Mann_a3 _atom_type.scat_Cromer_Mann_a4 _atom_type.scat_Cromer_Mann_b2 _atom_type.scat_Cromer_Mann_b3 _atom_type.scat_Cromer_Mann_b4 _atom_type.scat_Cromer_Mann_c
Category: atom_type
Mandatory: no
The Cromer-Mann scattering-factor coefficient b2 used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5.
Alias: _atom_type_scat_Cromer_Mann_b2 (cif_core.dic, 2.0.1)
Type: float
Dependent items: _atom_type.scat_Cromer_Mann_a1 _atom_type.scat_Cromer_Mann_a2 _atom_type.scat_Cromer_Mann_a3 _atom_type.scat_Cromer_Mann_a4 _atom_type.scat_Cromer_Mann_b1 _atom_type.scat_Cromer_Mann_b3 _atom_type.scat_Cromer_Mann_b4 _atom_type.scat_Cromer_Mann_c
Category: atom_type
Mandatory: no
The Cromer-Mann scattering-factor coefficient b3 used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5.
Alias: _atom_type_scat_Cromer_Mann_b3 (cif_core.dic, 2.0.1)
Type: float
Dependent items: _atom_type.scat_Cromer_Mann_a1 _atom_type.scat_Cromer_Mann_a2 _atom_type.scat_Cromer_Mann_a3 _atom_type.scat_Cromer_Mann_a4 _atom_type.scat_Cromer_Mann_b1 _atom_type.scat_Cromer_Mann_b2 _atom_type.scat_Cromer_Mann_b4 _atom_type.scat_Cromer_Mann_c
Category: atom_type
Mandatory: no
The Cromer-Mann scattering-factor coefficient b4 used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5.
Alias: _atom_type_scat_Cromer_Mann_b4 (cif_core.dic, 2.0.1)
Type: float
Dependent items: _atom_type.scat_Cromer_Mann_a1 _atom_type.scat_Cromer_Mann_a2 _atom_type.scat_Cromer_Mann_a3 _atom_type.scat_Cromer_Mann_a4 _atom_type.scat_Cromer_Mann_b1 _atom_type.scat_Cromer_Mann_b2 _atom_type.scat_Cromer_Mann_b3 _atom_type.scat_Cromer_Mann_c
Category: atom_type
Mandatory: no
The Cromer-Mann scattering-factor coefficient c used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5.
Alias: _atom_type_scat_Cromer_Mann_c (cif_core.dic, 2.0.1)
Type: float
Dependent items: _atom_type.scat_Cromer_Mann_a1 _atom_type.scat_Cromer_Mann_a2 _atom_type.scat_Cromer_Mann_a3 _atom_type.scat_Cromer_Mann_a4 _atom_type.scat_Cromer_Mann_b1 _atom_type.scat_Cromer_Mann_b2 _atom_type.scat_Cromer_Mann_b3 _atom_type.scat_Cromer_Mann_b4
Category: atom_type
Mandatory: no
The imaginary component of the anomalous-dispersion scattering factor, f'', in electrons for this atom type and the radiation identified by _diffrn_radiation_wavelength.id.
Alias: _atom_type_scat_dispersion_imag (cif_core.dic, 2.0.1)
Type: float
Dependent item: _atom_type.scat_dispersion_real
Category: atom_type
Mandatory: no
The real component of the anomalous-dispersion scattering factor, f', in electrons for this atom type and the radiation identified by _diffrn_radiation_wavelength.id.
Alias: _atom_type_scat_dispersion_real (cif_core.dic, 2.0.1)
Type: float
Dependent item: _atom_type.scat_dispersion_imag
Category: atom_type
Mandatory: no
The bound coherent scattering length in femtometres for the atom type at the isotopic composition used for the diffraction experiment.
Alias: _atom_type_scat_length_neutron (cif_core.dic, 2.0.1)
Type: text
Units: femtometres
Category: atom_type
Mandatory: no
Reference to the source of the scattering factors or scattering lengths used for this atom type.
Alias: _atom_type_scat_source (cif_core.dic, 2.0.1)
Type: text
Example:
International Tables Vol. IV Table 2.4.6B
Category: atom_type
Mandatory: no
A table of scattering factors as a function of sin theta over lambda. This table should be well commented to indicate the items present. Regularly formatted lists are strongly recommended.
Alias: _atom_type_scat_versus_stol_list (cif_core.dic, 2.0.1)
Type: text
| Name | Category | Mandatory |
|---|---|---|
| _atom_type.symbol | atom_type | yes |
| _atom_site.type_symbol | atom_site | yes |
| _atom_site_anisotrop.type_symbol | atom_site_anisotrop | yes |
| _chemical_conn_atom.type_symbol | chemical_conn_atom | yes |
| _chem_comp_atom.type_symbol | chem_comp_atom | yes |
| _phasing_MIR_der_site.atom_type_symbol | phasing_MIR_der_site | yes |
The code used to identify the atom species (singular or plural) representing this atom type. Normally this code is the element symbol. The code may be composed of any character except an underscore with the additional proviso that digits designate an oxidation state and must be followed by a + or - character.
Alias: _atom_type_symbol (cif_core.dic, 2.0.1)
Type: code
Child / Parent relations:
Examples:
| Example | Detail |
|---|---|
C |
|
Cu2+ |
|
H(SDS) |
|
dummy |
|
FeNi |
Data items in the AUDIT category record details about the creation and subsequent updating of the data block. Note that these items apply only to the creation and updating of the data block, and should not be confused with the data items in the JOURNAL category that record different stages in the publication of the material in the data block.
Mandatory: no
Keys: _audit.revision_id
Groups: inclusive_group audit_group
Examples:
| Example | Detail |
|---|---|
_audit.revision_id 1
_audit.creation_date '1992-12-08'
_audit.creation_method
; Created by hand from PDB entry 5HVP, from the J. Biol.
Chem. paper describing this structure and from
laboratory records
;
_audit.update_record
; 1992-12-09 adjusted to reflect comments from B. McKeever
1992-12-10 adjusted to reflect comments from H. Berman
1992-12-12 adjusted to reflect comments from K. Watenpaugh
;
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
_audit.creation_date 1991-03-20
_audit.creation_method from_xtal_archive_file_using_CIFIO
_audit.update_record
; 1991-04-09 text and data added by Tony Willis.
1991-04-15 rec'd by co-editor as manuscript HL0007.
1991-04-17 adjustments based on first referee report.
1991-04-18 adjustments based on second referee report.
;
|
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. |
Category: audit
Mandatory: no
A date that the data block was created. The date format is yyyy-mm-dd.
Alias: _audit_creation_date (cif_core.dic, 2.0.1)
Type: yyyy-mm-dd
Example:
1990-07-12
Category: audit
Mandatory: no
A description of how data were entered into the data block.
Alias: _audit_creation_method (cif_core.dic, 2.0.1)
Type: text
Example:
spawned by the program QBEE
Category: audit
Mandatory: yes
The value of _audit.revision_id must uniquely identify a record in the AUDIT list.
Type: code
Example:
rev1
Category: audit
Mandatory: no
A record of any changes to the data block. The update format is a date (yyyy-mm-dd) followed by a description of the changes. The latest update entry is added to the bottom of this record.
Alias: _audit_update_record (cif_core.dic, 2.0.1)
Type: text
Example:
1990-07-15 Updated by the Co-editor
Data items in the AUDIT_AUTHOR category record details about the author(s) of the data block.
Mandatory: no
Keys: _audit_author.name
Groups: inclusive_group audit_group
Examples:
| Example | Detail |
|---|---|
loop_
_audit_author.name
_audit_author.address
'Fitzgerald, Paula M.D.'
; Department of Biophysical Chemistry
Merck Research Laboratories
P. O. Box 2000, Ry80M203
Rahway, New Jersey 07065
USA
;
'McKeever, Brian M.'
; Department of Biophysical Chemistry
Merck Research Laboratories
P. O. Box 2000, Ry80M203
Rahway, New Jersey 07065
USA
;
'Van Middlesworth, J.F.'
; Department of Biophysical Chemistry
Merck Research Laboratories
P. O. Box 2000, Ry80M203
Rahway, New Jersey 07065
USA
;
'Springer, James P.'
; Department of Biophysical Chemistry
Merck Research Laboratories
P. O. Box 2000, Ry80M203
Rahway, New Jersey 07065
USA
;
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
Category: audit_author
Mandatory: no
The address of an author of this data block. If there are multiple authors, _audit_author.address is looped with _audit_author.name.
Alias: _audit_author_address (cif_core.dic, 2.0.1)
Type: text
Example:
Department
Institute
Street
City and postcode
COUNTRY
Category: audit_author
Mandatory: yes
The name of an author of this data block. If there are multiple authors, _audit_author.name is looped with _audit_author.address. The family name(s), followed by a comma and including any dynastic components, precedes the first name(s) or initial(s).
Alias: _audit_author_name (cif_core.dic, 2.0.1)
Type: line
Examples:
| Example | Detail |
|---|---|
Bleary, Percival R. |
|
O'Neil, F.K. |
|
Van den Bossche, G. |
|
Yang, D.-L. |
|
Simonov, Yu.A. |
Data items in the AUDIT_CONFORM category describe the dictionary versions against which the data names appearing in the current data block are conformant.
Mandatory: no
Keys: _audit_conform.dict_name _audit_conform.dict_version
Groups: inclusive_group audit_group
Examples:
| Example | Detail |
|---|---|
_audit_conform.dict_name cif_core.dic
_audit_conform.dict_version 2.3.1
_audit_conform.dict_location
ftp://ftp.iucr.org/pub/cif_core.2.3.1.dic
|
Example 1 - any file conforming to the current CIF core dictionary. |
Category: audit_conform
Mandatory: no
A file name or uniform resource locator (URL) for the dictionary to which the current data block conforms.
Alias: _audit_conform_dict_location (cif_core.dic, 2.0.1)
Type: text
Category: audit_conform
Mandatory: no
The string identifying the highest-level dictionary defining data names used in this file.
Alias: _audit_conform_dict_name (cif_core.dic, 2.0.1)
Type: text
Category: audit_conform
Mandatory: no
The version number of the dictionary to which the current data block conforms.
Alias: _audit_conform_dict_version (cif_core.dic, 2.0.1)
Type: text
Data items in the AUDIT_CONTACT_AUTHOR category record details about the name and address of the author to be contacted concerning the content of this data block.
Mandatory: no
Keys: _audit_contact_author.name
Groups: inclusive_group audit_group
Examples:
| Example | Detail |
|---|---|
_audit_contact_author.name 'Fitzgerald, Paula M.D.'
_audit_contact_author.address
; Department of Biophysical Chemistry
Merck Research Laboratories
PO Box 2000, Ry80M203
Rahway, New Jersey 07065
USA
;
_audit_contact_author.phone '1(908)5945510'
_audit_contact_author.fax '1(908)5946645'
_audit_contact_author.email 'paula_fitzgerald@merck.com'
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
Category: audit_contact_author
Mandatory: no
The mailing address of the author of the data block to whom correspondence should be addressed.
Alias: _audit_contact_author_address (cif_core.dic, 2.0.1)
Type: text
Example:
Department
Institute
Street
City and postcode
COUNTRY
Category: audit_contact_author
Mandatory: no
The electronic mail address of the author of the data block to whom correspondence should be addressed, in a form recognizable to international networks. The format of e-mail addresses is given in Section 3.4, Address Specification, of Internet Message Format, RFC 2822, P. Resnick (Editor), Network Standards Group, April 2001.
Alias: _audit_contact_author_email (cif_core.dic, 2.0.1)
Type: line
Examples:
| Example | Detail |
|---|---|
name@host.domain.country |
|
bm@iucr.org |
Category: audit_contact_author
Mandatory: no
The facsimile telephone number of the author of the data block to whom correspondence should be addressed. The recommended style starts with the international dialing prefix, followed by the area code in parentheses, followed by the local number with no spaces.
Alias: _audit_contact_author_fax (cif_core.dic, 2.0.1)
Type: line
Examples:
| Example | Detail |
|---|---|
12(34)9477334 |
|
12()349477334 |
Category: audit_contact_author
Mandatory: yes
The name of the author of the data block to whom correspondence should be addressed. The family name(s), followed by a comma and including any dynastic components, precedes the first name(s) or initial(s).
Alias: _audit_contact_author_name (cif_core.dic, 2.0.1)
Type: line
Examples:
| Example | Detail |
|---|---|
Bleary, Percival R. |
|
O'Neil, F.K. |
|
Van den Bossche, G. |
|
Yang, D.-L. |
|
Simonov, Yu.A. |
Category: audit_contact_author
Mandatory: no
The telephone number of the author of the data block to whom correspondence should be addressed. The recommended style starts with the international dialing prefix, followed by the area code in parentheses, followed by the local number and any extension number prefixed by 'x', with no spaces.
Alias: _audit_contact_author_phone (cif_core.dic, 2.0.1)
Type: line
Examples:
| Example | Detail |
|---|---|
12(34)9477330 |
|
12()349477330 |
|
12(34)9477330x5543 |
Data items in the CELL category record details about the crystallographic cell parameters.
Mandatory: no
Keys: _cell.entry_id
Groups: inclusive_group cell_group
Examples:
| Example | Detail |
|---|---|
_cell.entry_id '5HVP'
_cell.length_a 58.39
_cell.length_a_esd 0.05
_cell.length_b 86.70
_cell.length_b_esd 0.12
_cell.length_c 46.27
_cell.length_c_esd 0.06
_cell.angle_alpha 90.00
_cell.angle_beta 90.00
_cell.angle_gamma 90.00
_cell.volume 234237
_cell.details
; The cell parameters were refined every twenty frames during
data integration. The cell lengths given are the mean of
55 such refinements; the esds given are the root mean
square deviations of these 55 observations from that mean.
;
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
_cell.length_a 5.959
_cell.length_a_esd 0.001
_cell.length_b 14.956
_cell.length_b_esd 0.001
_cell.length_c 19.737
_cell.length_c_esd 0.003
_cell.angle_alpha 90.0
_cell.angle_beta 90.0
_cell.angle_gamma 90.0
_cell.volume 1759.0
_cell.volume_esd 0.3
|
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. |
Category: cell
Mandatory: no
Sub-category: cell_angle
Unit-cell angle alpha of the reported structure in degrees.
Alias: _cell_angle_alpha (cif_core.dic, 2.0.1)
Type: float
Type conditions: esd
Units: degrees
Dependent items: _cell.angle_beta _cell.angle_gamma
Related item: _cell.angle_alpha_esd (associated_esd)
Default value: 90.0
Range: [180.0, 180.0] [0.0, 180.0] [0.0, 0.0]
Category: cell
Mandatory: no
Sub-category: cell_angle_esd
The standard uncertainty (estimated standard deviation) of _cell.angle_alpha.
Type: float
Units: degrees
Dependent items: _cell.angle_beta_esd _cell.angle_gamma_esd
Related item: _cell.angle_alpha (associated_value)
Category: cell
Mandatory: no
Sub-category: cell_angle
Unit-cell angle beta of the reported structure in degrees.
Alias: _cell_angle_beta (cif_core.dic, 2.0.1)
Type: float
Type conditions: esd
Units: degrees
Dependent items: _cell.angle_alpha _cell.angle_gamma
Related item: _cell.angle_beta_esd (associated_esd)
Default value: 90.0
Range: [180.0, 180.0] [0.0, 180.0] [0.0, 0.0]
Category: cell
Mandatory: no
Sub-category: cell_angle_esd
The standard uncertainty (estimated standard deviation) of _cell.angle_beta.
Type: float
Units: degrees
Dependent items: _cell.angle_alpha_esd _cell.angle_gamma_esd
Related item: _cell.angle_beta (associated_value)
Category: cell
Mandatory: no
Sub-category: cell_angle
Unit-cell angle gamma of the reported structure in degrees.
Alias: _cell_angle_gamma (cif_core.dic, 2.0.1)
Type: float
Type conditions: esd
Units: degrees
Dependent items: _cell.angle_alpha _cell.angle_beta
Related item: _cell.angle_gamma_esd (associated_esd)
Default value: 90.0
Range: [180.0, 180.0] [0.0, 180.0] [0.0, 0.0]
Category: cell
Mandatory: no
Sub-category: cell_angle_esd
The standard uncertainty (estimated standard deviation) of _cell.angle_gamma.
Type: float
Units: degrees
Dependent items: _cell.angle_alpha_esd _cell.angle_beta_esd
Related item: _cell.angle_gamma (associated_value)
Mandatory: yes
This data item is a pointer to _entry.id in the ENTRY category.
Category: cell
Mandatory: no
A description of special aspects of the cell choice, noting possible alternative settings.
Alias: _cell_special_details (cif_core.dic, 2.0.1)
Type: text
Examples:
| Example | Detail |
|---|---|
pseudo-orthorhombic |
|
standard setting from 45 deg rotation around c |
Category: cell
Mandatory: no
The number of the formula units in the unit cell as specified by _chemical_formula.structural, _chemical_formula.moiety or _chemical_formula.sum.
Alias: _cell_formula_units_Z (cif_core.dic, 2.0.1)
Type: int
Range: [1, .] [1, 1]
Category: cell
Mandatory: no
Sub-category: cell_length
Unit-cell length a corresponding to the structure reported in angstroms.
Alias: _cell_length_a (cif_core.dic, 2.0.1)
Type: float
Type conditions: esd
Units: angstroms
Dependent items: _cell.length_b _cell.length_c
Related item: _cell.length_a_esd (associated_esd)
Range: [0.0, .] [0.0, 0.0]
Category: cell
Mandatory: no
Sub-category: cell_length_esd
The standard uncertainty (estimated standard deviation) of _cell.length_a.
Type: float
Units: angstroms
Dependent items: _cell.length_b_esd _cell.length_c_esd
Related item: _cell.length_a (associated_value)
Category: cell
Mandatory: no
Sub-category: cell_length
Unit-cell length b corresponding to the structure reported in angstroms.
Alias: _cell_length_b (cif_core.dic, 2.0.1)
Type: float
Type conditions: esd
Units: angstroms
Dependent items: _cell.length_a _cell.length_c
Related item: _cell.length_b_esd (associated_esd)
Range: [0.0, .] [0.0, 0.0]
Category: cell
Mandatory: no
Sub-category: cell_length_esd
The standard uncertainty (estimated standard deviation) of _cell.length_b.
Type: float
Units: angstroms
Dependent items: _cell.length_a_esd _cell.length_c_esd
Related item: _cell.length_b (associated_value)
Category: cell
Mandatory: no
Sub-category: cell_length
Unit-cell length c corresponding to the structure reported in angstroms.
Alias: _cell_length_c (cif_core.dic, 2.0.1)
Type: float
Type conditions: esd
Units: angstroms
Dependent items: _cell.length_a _cell.length_b
Related item: _cell.length_c_esd (associated_esd)
Range: [0.0, .] [0.0, 0.0]
Category: cell
Mandatory: no
Sub-category: cell_length_esd
The standard uncertainty (estimated standard deviation) of _cell.length_c.
Type: float
Units: angstroms
Dependent items: _cell.length_a_esd _cell.length_b_esd
Related item: _cell.length_c (associated_value)
Category: cell
Mandatory: no
Cell volume V in angstroms cubed. V = a b c (1 - cos2alpha - cos2beta - cos2gamma + 2 cosalpha cosbeta cosgamma)1/2 a = _cell.length_a b = _cell.length_b c = _cell.length_c alpha = _cell.angle_alpha beta = _cell.angle_beta gamma = _cell.angle_gamma
Alias: _cell_volume (cif_core.dic, 2.0.1)
Type: float
Type conditions: esd
Units: angstroms_cubed
Related item: _cell.volume_esd (associated_esd)
Range: [0.0, .] [0.0, 0.0]
Category: cell
Mandatory: no
The standard uncertainty (estimated standard deviation) of _cell.volume.
Type: float
Units: angstroms_cubed
Related item: _cell.volume (associated_value)
Category: cell
Mandatory: no
The number of the polymeric chains in a unit cell. In the case of heteropolymers, Z is the number of occurrences of the most populous chain. This data item is provided for compatibility with the original Protein Data Bank format, and only for that purpose.
Type: int
Range: [1, .] [1, 1]
Data items in the CELL_MEASUREMENT category record details about the measurement of the crystallographic cell parameters.
Mandatory: no
Keys: _cell_measurement.entry_id
Groups: inclusive_group cell_group
Examples:
| Example | Detail |
|---|---|
_cell_measurement.entry_id '5HVP'
_cell_measurement.temp 293
_cell_measurement.temp_esd 3
_cell_measurement.theta_min 11
_cell_measurement.theta_max 31
_cell_measurement.wavelength 1.54
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
_cell_measurement.temp 293
_cell_measurement.reflns_used 25
_cell_measurement.theta_min 25
_cell_measurement.theta_max 31
|
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. |
Mandatory: yes
This data item is a pointer to _entry.id in the ENTRY category.
Category: cell_measurement
Mandatory: no
The pressure in kilopascals at which the unit-cell parameters were measured (not the pressure at which the sample was synthesized).
Alias: _cell_measurement_pressure (cif_core.dic, 2.0.1)
Type: float
Type conditions: esd
Units: kilopascals
Related item: _cell_measurement.pressure_esd (associated_esd)
Category: cell_measurement
Mandatory: no
The standard uncertainty (estimated standard deviation) of _cell_measurement.pressure.
Type: float
Units: kilopascals
Related item: _cell_measurement.pressure (associated_value)
Category: cell_measurement
Mandatory: no
Description of the radiation used to measure the unit-cell data. See also _cell_measurement.wavelength.
Alias: _cell_measurement_radiation (cif_core.dic, 2.0.1)
Type: line
Examples:
| Example | Detail |
|---|---|
neutron |
|
Cu K\a |
|
synchrotron |
Category: cell_measurement
Mandatory: no
The total number of reflections used to determine the unit cell. These reflections may be specified as CELL_MEASUREMENT_REFLN data items.
Alias: _cell_measurement_reflns_used (cif_core.dic, 2.0.1)
Type: int
Category: cell_measurement
Mandatory: no
The temperature in kelvins at which the unit-cell parameters were measured (not the temperature of synthesis).
Alias: _cell_measurement_temperature (cif_core.dic, 2.0.1)
Type: float
Type conditions: esd
Units: kelvins
Related item: _cell_measurement.temp_esd (associated_esd)
Range: [0.0, .] [0.0, 0.0]
Category: cell_measurement
Mandatory: no
The standard uncertainty (estimated standard deviation) of _cell_measurement.temp.
Type: float
Units: kelvins
Related item: _cell_measurement.temp (associated_value)
Category: cell_measurement
Mandatory: no
The maximum theta angle of reflections used to measure the unit cell in degrees.
Alias: _cell_measurement_theta_max (cif_core.dic, 2.0.1)
Type: float
Units: degrees
Range: [90.0, 90.0] [0.0, 90.0] [0.0, 0.0]
Category: cell_measurement
Mandatory: no
The minimum theta angle of reflections used to measure the unit cell in degrees.
Alias: _cell_measurement_theta_min (cif_core.dic, 2.0.1)
Type: float
Units: degrees
Range: [90.0, 90.0] [0.0, 90.0] [0.0, 0.0]
Category: cell_measurement
Mandatory: no
The wavelength in angstroms of the radiation used to measure the unit cell. If this is not specified, the wavelength is assumed to be that specified in the category DIFFRN_RADIATION_WAVELENGTH.
Alias: _cell_measurement_wavelength (cif_core.dic, 2.0.1)
Type: float
Units: angstroms
Range: [0.0, .] [0.0, 0.0]
Data items in the CELL_MEASUREMENT_REFLN category record details about the reflections used to determine the crystallographic cell parameters. The CELL_MEASUREMENT_REFLN data items would in general be used only for diffractometer data.
Mandatory: no
Keys: _cell_measurement_refln.index_h _cell_measurement_refln.index_k _cell_measurement_refln.index_l
Groups: inclusive_group cell_group
Examples:
| Example | Detail |
|---|---|
loop_
_cell_measurement_refln.index_h
_cell_measurement_refln.index_k
_cell_measurement_refln.index_l
_cell_measurement_refln.theta
-2 4 1 8.67
0 3 2 9.45
3 0 2 9.46
-3 4 1 8.93
-2 1 -2 7.53
10 0 0 23.77
0 10 0 23.78
-5 4 1 11.14
# - - - - data truncated for brevity - - - -
|
Example 1 - extracted from the CAD-4 listing of Rb~2~S~2~O~6~ at room temperature (unpublished). |
Category: cell_measurement_refln
Mandatory: yes
Sub-category: miller_index
Miller index h of a reflection used for measurement of the unit cell.
Alias: _cell_measurement_refln_index_h (cif_core.dic, 2.0.1)
Type: int
Dependent items: _cell_measurement_refln.index_k _cell_measurement_refln.index_l
Category: cell_measurement_refln
Mandatory: yes
Sub-category: miller_index
Miller index k of a reflection used for measurement of the unit cell.
Alias: _cell_measurement_refln_index_k (cif_core.dic, 2.0.1)
Type: int
Dependent items: _cell_measurement_refln.index_h _cell_measurement_refln.index_l
Category: cell_measurement_refln
Mandatory: yes
Sub-category: miller_index
Miller index l of a reflection used for measurement of the unit cell.
Alias: _cell_measurement_refln_index_l (cif_core.dic, 2.0.1)
Type: int
Dependent items: _cell_measurement_refln.index_h _cell_measurement_refln.index_k
Category: cell_measurement_refln
Mandatory: no
Theta angle for a reflection used for measurement of the unit cell in degrees.
Alias: _cell_measurement_refln_theta (cif_core.dic, 2.0.1)
Type: float
Units: degrees
Range: [90.0, 90.0] [0.0, 90.0] [0.0, 0.0]
Data items in the CHEM_COMP category give details about each of the chemical components from which the relevant chemical structures can be constructed, such as name, mass or charge. The related categories CHEM_COMP_ATOM, CHEM_COMP_BOND, CHEM_COMP_ANGLE etc. describe the detailed geometry of these chemical components.
Mandatory: no
Keys: _chem_comp.id
Groups: inclusive_group chem_comp_group
Examples:
| Example | Detail |
|---|---|
loop_
_chem_comp.id
_chem_comp.model_source
_chem_comp.name
phe '1987 Protin/Prolsq Ideals file' phenylalanine
val '1987 Protin/Prolsq Ideals file' alanine
# - - - - data truncated for brevity - - - -
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
Category: chem_comp
Mandatory: no
The formula for the chemical component. Formulae are written according to the following rules: (1) Only recognized element symbols may be used. (2) Each element symbol is followed by a 'count' number. A count of '1' may be omitted. (3) A space or parenthesis must separate each cluster of (element symbol + count), but in general parentheses are not used. (4) The order of elements depends on whether carbon is present or not. If carbon is present, the order should be: C, then H, then the other elements in alphabetical order of their symbol. If carbon is not present, the elements are listed purely in alphabetic order of their symbol. This is the 'Hill' system used by Chemical Abstracts.
Type: text
Examples:
| Example | Detail |
|---|---|
C18 H19 N7 O8 S |
Category: chem_comp
Mandatory: no
Formula mass in daltons of the chemical component.
Type: float
Range: [1.0, .] [1.0, 1.0]
| Name | Category | Mandatory |
|---|---|---|
| _chem_comp.id | chem_comp | yes |
| _atom_site.label_comp_id | atom_site | no |
| _chem_comp.mon_nstd_parent_comp_id | chem_comp | no |
| _chem_comp_atom.comp_id | chem_comp_atom | yes |
| _chem_comp_angle.comp_id | chem_comp_angle | yes |
| _chem_comp_bond.comp_id | chem_comp_bond | yes |
| _chem_comp_chir.comp_id | chem_comp_chir | yes |
| _chem_comp_chir_atom.comp_id | chem_comp_chir_atom | yes |
| _chem_comp_plane.comp_id | chem_comp_plane | yes |
| _chem_comp_plane_atom.comp_id | chem_comp_plane_atom | yes |
| _chem_comp_tor.comp_id | chem_comp_tor | yes |
| _chem_comp_tor_value.comp_id | chem_comp_tor_value | yes |
| _entity_poly_seq.mon_id | entity_poly_seq | yes |
| _geom_angle.atom_site_label_comp_id_1 | geom_angle | no |
| _geom_angle.atom_site_label_comp_id_2 | geom_angle | no |
| _geom_angle.atom_site_label_comp_id_3 | geom_angle | no |
| _geom_bond.atom_site_label_comp_id_1 | geom_bond | no |
| _geom_bond.atom_site_label_comp_id_2 | geom_bond | no |
| _geom_contact.atom_site_label_comp_id_1 | geom_contact | no |
| _geom_contact.atom_site_label_comp_id_2 | geom_contact | no |
| _geom_hbond.atom_site_label_comp_id_A | geom_hbond | no |
| _geom_hbond.atom_site_label_comp_id_D | geom_hbond | no |
| _geom_hbond.atom_site_label_comp_id_H | geom_hbond | no |
| _geom_torsion.atom_site_label_comp_id_1 | geom_torsion | no |
| _geom_torsion.atom_site_label_comp_id_2 | geom_torsion | no |
| _geom_torsion.atom_site_label_comp_id_3 | geom_torsion | no |
| _geom_torsion.atom_site_label_comp_id_4 | geom_torsion | no |
| _struct_conf.beg_label_comp_id | struct_conf | yes |
| _struct_conf.end_label_comp_id | struct_conf | yes |
| _struct_conn.ptnr1_label_comp_id | struct_conn | yes |
| _struct_conn.ptnr2_label_comp_id | struct_conn | yes |
| _struct_mon_nucl.label_comp_id | struct_mon_nucl | yes |
| _struct_mon_prot.label_comp_id | struct_mon_prot | yes |
| _struct_mon_prot_cis.label_comp_id | struct_mon_prot_cis | yes |
| _struct_ncs_dom_lim.beg_label_comp_id | struct_ncs_dom_lim | yes |
| _struct_ncs_dom_lim.end_label_comp_id | struct_ncs_dom_lim | yes |
| _struct_ref_seq_dif.db_mon_id | struct_ref_seq_dif | yes |
| _struct_ref_seq_dif.mon_id | struct_ref_seq_dif | yes |
| _struct_sheet_range.beg_label_comp_id | struct_sheet_range | yes |
| _struct_sheet_range.end_label_comp_id | struct_sheet_range | yes |
| _struct_site_gen.label_comp_id | struct_site_gen | yes |
The value of _chem_comp.id must uniquely identify each item in the CHEM_COMP list. For protein polymer entities, this is the three-letter code for the amino acid. For nucleic acid polymer entities, this is the one-letter code for the base.
Type: ucode
Child / Parent relations:
Examples:
| Example | Detail |
|---|---|
ala |
|
val |
|
A |
|
C |
Category: chem_comp
Mandatory: no
A description of special aspects of the generation of the coordinates for the model of the component.
Type: text
Example:
geometry idealized but not minimized
Category: chem_comp
Mandatory: no
A pointer to an external reference file from which the atomic description of the component is taken.
Type: line
Category: chem_comp
Mandatory: no
The source of the coordinates for the model of the component.
Type: text
Examples:
| Example | Detail |
|---|---|
CSD entry ABCDEF |
|
built using Quanta/Charmm |
Category: chem_comp
Mandatory: no
A description of the class of a nonstandard monomer if the nonstandard monomer represents a modification of a standard monomer.
Type: text
Examples:
| Example | Detail |
|---|---|
iodinated base |
|
phosphorylated amino acid |
|
brominated base |
|
modified amino acid |
|
glycosylated amino acid |
Category: chem_comp
Mandatory: no
A description of special details of a nonstandard monomer.
Type: text
Category: chem_comp
Mandatory: no
'yes' indicates that this is a 'standard' monomer, 'no' indicates that it is 'nonstandard'. Nonstandard monomers should be described in more detail using the _chem_comp.mon_nstd_parent, _chem_comp.mon_nstd_class and _chem_comp.mon_nstd_details data items.
Type: ucode
Default value: no
Enumeration values:
| Value | Detail |
|---|---|
no |
the monomer is nonstandard |
n |
abbreviation for "no" |
yes |
the monomer is standard |
y |
abbreviation for "yes" |
Category: chem_comp
Mandatory: no
The name of the parent monomer of the nonstandard monomer, if the nonstandard monomer represents a modification of a standard monomer.
Type: code
Examples:
| Example | Detail |
|---|---|
tyrosine |
|
cytosine |
Mandatory: no
The identifier for the parent component of the nonstandard component. This data item is a pointer to _chem_comp.id in the CHEM_COMP category.
Category: chem_comp
Mandatory: no
The full name of the component.
Type: line
Examples:
| Example | Detail |
|---|---|
alanine |
|
valine |
|
adenine |
|
cytosine |
Category: chem_comp
Mandatory: no
The total number of atoms in the component.
Type: int
Range: [1, .] [1, 1]
Category: chem_comp
Mandatory: no
The number of non-hydrogen atoms in the component.
Type: int
Range: [1, .] [1, 1]
Category: chem_comp
Mandatory: no
For standard polymer components, the one-letter code for the component. If there is not a standard one-letter code for this component, or if this is a non-polymer component, the one-letter code should be given as 'X'. This code may be preceded by a '+' character to indicate that the component is a modification of a standard component.
Type: uchar1
Examples:
| Example | Detail |
|---|---|
A |
alanine or adenine |
B |
ambiguous asparagine/aspartic acid |
R |
arginine |
N |
asparagine |
D |
aspartic acid |
C |
cysteine or cystine or cytosine |
Q |
glutamine |
E |
glutamic acid |
Z |
ambiguous glutamine/glutamic acid |
G |
glycine or guanine |
H |
histidine |
I |
isoleucine |
L |
leucine |
K |
lysine |
M |
methionine |
F |
phenylalanine |
P |
proline |
S |
serine |
T |
threonine or thymine |
W |
tryptophan |
Y |
tyrosine |
V |
valine |
U |
uracil |
O |
water |
X |
other |
Category: chem_comp
Mandatory: no
For standard polymer components, the three-letter code for the component. If there is not a standard three-letter code for this component, or if this is a non-polymer component, the three-letter code should be given as 'UNK'. This code may be preceded by a '+' character to indicate that the component is a modification of a standard component.
Type: uchar3
Examples:
| Example | Detail |
|---|---|
ALA |
alanine |
ARG |
arginine |
ASN |
asparagine |
ASP |
aspartic acid |
ASX |
ambiguous asparagine/aspartic acid |
CYS |
cysteine |
GLN |
glutamine |
GLU |
glutamic acid |
GLY |
glycine |
GLX |
ambiguous glutamine/glutamic acid |
HIS |
histidine |
ILE |
isoleucine |
LEU |
leucine |
LYS |
lysine |
MET |
methionine |
PHE |
phenylalanine |
PRO |
proline |
SER |
serine |
THR |
threonine |
TRP |
tryptophan |
TRY |
tyrosine |
VAL |
valine |
1MA |
1-methyladenosine |
5MC |
5-methylcytosine |
OMC |
2(prime)-O-methylcytodine |
1MG |
1-methylguanosine |
2MG |
N(2)-methylguanosine |
M2G |
N(2)-dimethylguanosine |
7MG |
7-methylguanosine |
0MG |
2(prime)-O-methylguanosine |
H2U |
dihydrouridine |
5MU |
ribosylthymidine |
PSU |
pseudouridine |
ACE |
acetic acid |
FOR |
formic acid |
HOH |
water |
UNK |
other |
| Name | Category | Mandatory |
|---|---|---|
| _chem_comp.type | chem_comp | yes |
| _chem_comp_link.type_comp_1 | chem_comp_link | yes |
| _chem_comp_link.type_comp_2 | chem_comp_link | yes |
For standard polymer components, the type of the monomer. Note that monomers that will form polymers are of three types: linking monomers, monomers with some type of N-terminal (or 5') cap and monomers with some type of C-terminal (or 3') cap.
Type: uline
Child / Parent relations:
| Child | Parent |
|---|---|
| _chem_comp_link.type_comp_1 | _chem_comp.type |
| _chem_comp_link.type_comp_2 | _chem_comp.type |
Enumeration values:
| Value | Detail |
|---|---|
D-peptide linking |
|
L-peptide linking |
|
D-peptide NH3 amino terminus |
|
L-peptide NH3 amino terminus |
|
D-peptide COOH carboxy terminus |
|
L-peptide COOH carboxy terminus |
|
DNA linking |
|
RNA linking |
|
DNA OH 5 prime terminus |
|
RNA OH 5 prime terminus |
|
DNA OH 3 prime terminus |
|
RNA OH 3 prime terminus |
|
D-saccharide 1,4 and 1,4 linking |
|
L-saccharide 1,4 and 1,4 linking |
|
D-saccharide 1,4 and 1,6 linking |
|
L-saccharide 1,4 and 1,6 linking |
|
L-saccharide |
|
D-saccharide |
|
saccharide |
|
non-polymer |
|
other |
Data items in the CHEM_COMP_ANGLE category record details about angles in a chemical component. Angles are designated by three atoms, with the second atom forming the vertex of the angle. Target values may be specified as angles in degrees, as a distance between the first and third atoms, or both.
Mandatory: no
Keys: _chem_comp_angle.comp_id _chem_comp_angle.atom_id_1 _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3
Groups: inclusive_group chem_comp_group
Examples:
| Example | Detail |
|---|---|
loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_dist
phe N CA C xxx.xx x.xx
phe CA C O xxx.xx x.xx
phe CB CA C xxx.xx x.xx
phe CB CA N xxx.xx x.xx
phe CA CB CG xxx.xx x.xx
phe CB CG CD1 xxx.xx x.xx
phe CB CG CD2 xxx.xx x.xx
phe CD1 CG CD2 xxx.xx x.xx
phe CG CD1 CE1 xxx.xx x.xx
phe CD1 CE1 CZ xxx.xx x.xx
phe CE1 CZ CE2 xxx.xx x.xx
phe CZ CE2 CD2 xxx.xx x.xx
phe CG CD2 CE2 xxx.xx x.xx
val N CA C xxx.xx x.xx
val CA C O xxx.xx x.xx
val CB CA C xxx.xx x.xx
val CB CA N xxx.xx x.xx
val CA CB CG1 xxx.xx x.xx
val CA CB CG2 xxx.xx x.xx
val CG1 CB CG2 xxx.xx x.xx
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
Mandatory: yes
The ID of the first of the three atoms that define the angle. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category.
Dependent items: _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3
Mandatory: yes
The ID of the second of the three atoms that define the angle. The second atom is taken to be the apex of the angle. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category.
Dependent items: _chem_comp_angle.atom_id_1 _chem_comp_angle.atom_id_3
Mandatory: yes
The ID of the third of the three atoms that define the angle. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category.
Dependent items: _chem_comp_angle.atom_id_1 _chem_comp_angle.atom_id_2
Mandatory: yes
This data item is a pointer to _chem_comp.id in the CHEM_COMP category.
Category: chem_comp_angle
Mandatory: no
The value that should be taken as the target value for the angle associated with the specified atoms, expressed in degrees.
Type: float
Type conditions: esd
Units: degrees
Related item: _chem_comp_angle.value_angle_esd (associated_esd)
Range: [180.0, 180.0] [0.0, 180.0] [0.0, 0.0]
Category: chem_comp_angle
Mandatory: no
The standard uncertainty (estimated standard deviation) of _chem_comp_angle.value_angle.
Type: float
Units: degrees
Related item: _chem_comp_angle.value_angle (associated_value)
Range: [180.0, 180.0] [0.0, 180.0] [0.0, 0.0]
Category: chem_comp_angle
Mandatory: no
The value that should be taken as the target value for the angle associated with the specified atoms, expressed as the distance between the atoms specified by _chem_comp_angle.atom_id_1 and _chem_comp_angle.atom_id_3.
Type: float
Type conditions: esd
Units: angstroms
Related item: _chem_comp_angle.value_dist_esd (associated_esd)
Range: [0.0, .] [0.0, 0.0]
Category: chem_comp_angle
Mandatory: no
The standard uncertainty (estimated standard deviation) of _chem_comp_angle.value_dist.
Type: float
Units: angstroms
Related item: _chem_comp_angle.value_dist (associated_value)
Range: [0.0, .] [0.0, 0.0]
Data items in the CHEM_COMP_ATOM category record details about the atoms in a chemical component. Specifying the atomic coordinates for the components in this category is an alternative to specifying the structure of the component via bonds, angles, planes etc. in the appropriate CHEM_COMP subcategories.
Mandatory: no
Keys: _chem_comp_atom.comp_id _chem_comp_atom.atom_id
Groups: inclusive_group chem_comp_group
Examples:
| Example | Detail |
|---|---|
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.substruct_code
_chem_comp_atom.model_Cartn_x
_chem_comp_atom.model_Cartn_y
_chem_comp_atom.model_Cartn_z
phe N N main 1.20134 0.84658 0.00000
phe CA C main 0.00000 0.00000 0.00000
phe C C main -1.25029 0.88107 0.00000
phe O O main -2.18525 0.66029 -0.78409
phe CB C side 0.00662 -1.03603 1.11081
phe CG C side 0.03254 -0.49711 2.50951
phe CD1 C side -1.15813 -0.12084 3.13467
phe CE1 C side -1.15720 0.38038 4.42732
phe CZ C side 0.05385 0.51332 5.11032
phe CE2 C side 1.26137 0.11613 4.50975
phe CD2 C side 1.23668 -0.38351 3.20288
val N N main 1.20134 0.84658 0.00000
val CA C main 0.00000 0.00000 0.00000
val C C main -1.25029 0.88107 0.00000
val O O main -2.18525 0.66029 -0.78409
val CB C side 0.05260 -0.99339 1.17429
val CG1 C side -0.13288 -0.31545 2.52668
val CG2 C side -0.94265 -2.12930 0.99811
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
Category: chem_comp_atom
Mandatory: no
An alternative identifier for the atom. This data item would be used in cases where alternative nomenclatures exist for labelling atoms in a group.
Type: line
| Name | Category | Mandatory |
|---|---|---|
| _chem_comp_atom.atom_id | chem_comp_atom | yes |
| _atom_site.label_atom_id | atom_site | no |
| _chem_comp_angle.atom_id_1 | chem_comp_angle | yes |
| _chem_comp_angle.atom_id_2 | chem_comp_angle | yes |
| _chem_comp_angle.atom_id_3 | chem_comp_angle | yes |
| _chem_comp_bond.atom_id_1 | chem_comp_bond | yes |
| _chem_comp_bond.atom_id_2 | chem_comp_bond | yes |
| _chem_comp_chir.atom_id | chem_comp_chir | yes |
| _chem_comp_chir_atom.atom_id | chem_comp_chir_atom | yes |
| _chem_comp_plane_atom.atom_id | chem_comp_plane_atom | yes |
| _chem_comp_tor.atom_id_1 | chem_comp_tor | yes |
| _chem_comp_tor.atom_id_2 | chem_comp_tor | yes |
| _chem_comp_tor.atom_id_3 | chem_comp_tor | yes |
| _chem_comp_tor.atom_id_4 | chem_comp_tor | yes |
| _geom_angle.atom_site_label_atom_id_1 | geom_angle | no |
| _geom_angle.atom_site_label_atom_id_2 | geom_angle | no |
| _geom_angle.atom_site_label_atom_id_3 | geom_angle | no |
| _geom_bond.atom_site_label_atom_id_1 | geom_bond | no |
| _geom_bond.atom_site_label_atom_id_2 | geom_bond | no |
| _geom_contact.atom_site_label_atom_id_1 | geom_contact | no |
| _geom_contact.atom_site_label_atom_id_2 | geom_contact | no |
| _geom_hbond.atom_site_label_atom_id_A | geom_hbond | no |
| _geom_hbond.atom_site_label_atom_id_D | geom_hbond | no |
| _geom_hbond.atom_site_label_atom_id_H | geom_hbond | no |
| _geom_torsion.atom_site_label_atom_id_1 | geom_torsion | no |
| _geom_torsion.atom_site_label_atom_id_2 | geom_torsion | no |
| _geom_torsion.atom_site_label_atom_id_3 | geom_torsion | no |
| _geom_torsion.atom_site_label_atom_id_4 | geom_torsion | no |
| _struct_conn.ptnr1_label_atom_id | struct_conn | yes |
| _struct_conn.ptnr2_label_atom_id | struct_conn | yes |
| _struct_sheet_hbond.range_1_beg_label_atom_id | struct_sheet_hbond | yes |
| _struct_sheet_hbond.range_1_end_label_atom_id | struct_sheet_hbond | yes |
| _struct_sheet_hbond.range_2_beg_label_atom_id | struct_sheet_hbond | yes |
| _struct_sheet_hbond.range_2_end_label_atom_id | struct_sheet_hbond | yes |
| _struct_site_gen.label_atom_id | struct_site_gen | yes |
The value of _chem_comp_atom.atom_id must uniquely identify each atom in each monomer in the CHEM_COMP_ATOM list. The atom identifiers need not be unique over all atoms in the data block; they need only be unique for each atom in a component. Note that this item need not be a number; it can be any unique identifier.
Type: atcode
Child / Parent relations:
Category: chem_comp_atom
Mandatory: no
The net integer charge assigned to this atom. This is the formal charge assignment normally found in chemical diagrams.
Type: int
Default value: 0
Range: [8, 8] [-8, 8] [-8, -8]
Examples:
| Example | Detail |
|---|---|
1 |
for an ammonium nitrogen |
-1 |
for a chloride ion |
Category: chem_comp_atom
Mandatory: no
Sub-category: cartesian_coordinate
The x component of the coordinates for this atom in this component specified as orthogonal angstroms. The choice of reference axis frame for the coordinates is arbitrary. The set of coordinates input for the entity here is intended to correspond to the atomic model used to generate restraints for structure refinement, not to atom sites in the ATOM_SITE list.
Type: float
Type conditions: esd
Units: angstroms
Dependent items: _chem_comp_atom.model_Cartn_y _chem_comp_atom.model_Cartn_z
Related item: _chem_comp_atom.model_Cartn_x_esd (associated_esd)
Category: chem_comp_atom
Mandatory: no
Sub-category: cartesian_coordinate_esd
The standard uncertainty (estimated standard deviation) of _chem_comp_atom.model_Cartn_x.
Type: float
Units: angstroms
Dependent items: _chem_comp_atom.model_Cartn_y_esd _chem_comp_atom.model_Cartn_z_esd
Related item: _chem_comp_atom.model_Cartn_x (associated_value)
Category: chem_comp_atom
Mandatory: no
Sub-category: cartesian_coordinate
The y component of the coordinates for this atom in this component specified as orthogonal angstroms. The choice of reference axis frame for the coordinates is arbitrary. The set of coordinates input for the entity here is intended to correspond to the atomic model used to generate restraints for structure refinement, not to atom sites in the ATOM_SITE list.
Type: float
Type conditions: esd
Units: angstroms
Dependent items: _chem_comp_atom.model_Cartn_x _chem_comp_atom.model_Cartn_z
Related item: _chem_comp_atom.model_Cartn_y_esd (associated_esd)
Category: chem_comp_atom
Mandatory: no
Sub-category: cartesian_coordinate_esd
The standard uncertainty (estimated standard deviation) of _chem_comp_atom.model_Cartn_y.
Type: float
Units: angstroms
Dependent items: _chem_comp_atom.model_Cartn_x_esd _chem_comp_atom.model_Cartn_z_esd
Related item: _chem_comp_atom.model_Cartn_y (associated_value)
Category: chem_comp_atom
Mandatory: no
Sub-category: cartesian_coordinate
The z component of the coordinates for this atom in this component specified as orthogonal angstroms. The choice of reference axis frame for the coordinates is arbitrary. The set of coordinates input for the entity here is intended to correspond to the atomic model used to generate restraints for structure refinement, not to atom sites in the ATOM_SITE list.
Type: float
Type conditions: esd
Units: angstroms
Dependent items: _chem_comp_atom.model_Cartn_x _chem_comp_atom.model_Cartn_y
Related item: _chem_comp_atom.model_Cartn_z_esd (associated_esd)
Category: chem_comp_atom
Mandatory: no
Sub-category: cartesian_coordinate_esd
The standard uncertainty (estimated standard deviation) of _chem_comp_atom.model_Cartn_z.
Type: float
Units: angstroms
Dependent items: _chem_comp_atom.model_Cartn_x_esd _chem_comp_atom.model_Cartn_y_esd
Related item: _chem_comp_atom.model_Cartn_z (associated_value)
Mandatory: yes
This data item is a pointer to _chem_comp.id in the CHEM_COMP category.
Category: chem_comp_atom
Mandatory: no
The partial charge assigned to this atom.
Type: float
Category: chem_comp_atom
Mandatory: no
This data item assigns the atom to a substructure of the component, if appropriate.
Type: ucode
Enumeration values:
| Value | Detail |
|---|---|
main |
main chain of an amino acid |
side |
side chain of an amino acid |
base |
base of a nucleic acid |
phos |
phosphate of a nucleic acid |
sugar |
sugar of a nucleic acid |
none |
not appropriate for this monomer |
Mandatory: yes
This data item is a pointer to _atom_type.symbol in the ATOM_TYPE category.
Data items in the CHEM_COMP_BOND category record details about the bonds between atoms in a chemical component. Target values may be specified as bond orders, as a distance between the two atoms, or both.
Mandatory: no
Keys: _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2
Groups: inclusive_group chem_comp_group
Examples:
| Example | Detail |
|---|---|
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
phe N CA sing
phe CA C sing
phe C O doub
phe CB CA sing
phe CB CG sing
phe CG CD1 arom
phe CD1 CE1 arom
phe CE1 CZ arom
phe CZ CE2 arom
phe CE2 CD2 arom
phe CD2 CG arom
val N CA sing
val CA C sing
val C O doub
val CB CA sing
val CB CG1 sing
val CB CG2 sing
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
Mandatory: yes
The ID of the first of the two atoms that define the bond. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category.
Dependent item: _chem_comp_bond.atom_id_2
Mandatory: yes
The ID of the second of the two atoms that define the bond. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category.
Dependent item: _chem_comp_bond.atom_id_1
Mandatory: yes
This data item is a pointer to _chem_comp.id in the CHEM_COMP category.
Category: chem_comp_bond
Mandatory: no
The value that should be taken as the target for the chemical bond associated with the specified atoms, expressed as a bond order.
Type: ucode
Default value: sing
Enumeration values:
| Value | Detail |
|---|---|
sing |
single bond |
doub |
double bond |
trip |
triple bond |
quad |
quadruple bond |
arom |
aromatic bond |
poly |
polymeric bond |
delo |
delocalized double bond |
pi |
pi bond |
Category: chem_comp_bond
Mandatory: no
The value that should be taken as the target for the chemical bond associated with the specified atoms, expressed as a distance.
Type: float
Type conditions: esd
Units: angstroms
Related item: _chem_comp_bond.value_dist_esd (associated_esd)
Range: [0.0, .] [0.0, 0.0]
Category: chem_comp_bond
Mandatory: no
The standard uncertainty (estimated standard deviation) of _chem_comp_bond.value_dist.
Type: float
Units: angstroms
Related item: _chem_comp_bond.value_dist (associated_value)
Range: [0.0, .] [0.0, 0.0]
Data items in the CHEM_COMP_CHIR category provide details about the chiral centres in a chemical component. The atoms bonded to the chiral atom are specified in the CHEM_COMP_CHIR_ATOM category.
Mandatory: no
Keys: _chem_comp_chir.comp_id _chem_comp_chir.id
Groups: inclusive_group chem_comp_group
Examples:
| Example | Detail |
|---|---|
loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id
phe phe1 CA
val val1 CA
# - - - - data truncated for brevity - - - -
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
Mandatory: yes
The ID of the atom that is a chiral centre. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category.
Category: chem_comp_chir
Mandatory: no
The chiral configuration of the atom that is a chiral centre.
Type: ucode
Enumeration values:
| Value | Detail |
|---|---|
R |
absolute configuration R |
S |
absolute configuration S |
| Name | Category | Mandatory |
|---|---|---|
| _chem_comp_chir.id | chem_comp_chir | yes |
| _chem_comp_chir_atom.chir_id | chem_comp_chir_atom | yes |
The value of _chem_comp_chir.id must uniquely identify a record in the CHEM_COMP_CHIR list.
Type: code
Child / Parent relations:
| Child | Parent |
|---|---|
| _chem_comp_chir_atom.chir_id | _chem_comp_chir.id |
Mandatory: yes
This data item is a pointer to _chem_comp.id in the CHEM_COMP category.
Category: chem_comp_chir
Mandatory: no
The total number of atoms bonded to the atom specified by _chem_comp_chir.atom_id.
Type: int
Category: chem_comp_chir
Mandatory: no
The number of non-hydrogen atoms bonded to the atom specified by _chem_comp_chir.atom_id.
Type: int
Category: chem_comp_chir
Mandatory: no
A flag to indicate whether a chiral volume should match the standard value in both magnitude and sign, or in magnitude only.
Type: ucode
Enumeration values:
| Value | Detail |
|---|---|
sign |
match magnitude and sign |
nosign |
match magnitude only |
Category: chem_comp_chir
Mandatory: no
The chiral volume, Vc, for chiral centres that involve a chiral atom bonded to three non-hydrogen atoms and one hydrogen atom. Vc = V1 * (V2 X V3) V1 = the vector distance from the atom specified by _chem_comp_chir.atom_id to the first atom in the CHEM_COMP_CHIR_ATOM list V2 = the vector distance from the atom specified by _chem_comp_chir.atom_id to the second atom in the CHEM_COMP_CHIR_ATOM list V3 = the vector distance from the atom specified by _chem_comp_chir.atom_id to the third atom in the CHEM_COMP_CHIR_ATOM list * = the vector dot product X = the vector cross product
Type: float
Type conditions: esd
Units: angstroms_cubed
Related item: _chem_comp_chir.volume_three_esd (associated_esd)
Category: chem_comp_chir
Mandatory: no
The standard uncertainty (estimated standard deviation) of _chem_comp_chir.volume_three.
Type: float
Units: angstroms_cubed
Related item: _chem_comp_chir.volume_three (associated_value)
Data items in the CHEM_COMP_CHIR_ATOM category enumerate the atoms bonded to a chiral atom within a chemical component.
Mandatory: no
Keys: _chem_comp_chir_atom.chir_id _chem_comp_chir_atom.atom_id _chem_comp_chir_atom.comp_id
Groups: inclusive_group chem_comp_group
Examples:
| Example | Detail |
|---|---|
loop_
_chem_comp_chir_atom.comp_id
_chem_comp_chir_atom.chir_id
_chem_comp_chir_atom.atom_id
phe 1 N
phe 1 C
phe 1 CB
val 1 N
val 1 C
val 1 CB
# - - - - data truncated for brevity - - - -
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
Mandatory: yes
The ID of an atom bonded to the chiral atom. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category.
Mandatory: yes
This data item is a pointer to _chem_comp_chir.id in the CHEM_COMP_CHIR category.
Mandatory: yes
This data item is a pointer to _chem_comp.id in the CHEM_COMP category.
Category: chem_comp_chir_atom
Mandatory: no
The standard uncertainty (estimated standard deviation) of the position of this atom from the plane defined by all of the atoms in the plane.
Type: float
Units: angstroms
Data items in the CHEM_COMP_LINK category give details about the links between chemical components.
Mandatory: no
Keys: _chem_comp_link.link_id
Groups: inclusive_group chem_link_group
Mandatory: yes
This data item is a pointer to _chem_link.id in the CHEM_LINK category.
Category: chem_comp_link
Mandatory: no
A description of special aspects of a link between chemical components in the structure.
Type: text
Mandatory: yes
The type of the first of the two components joined by the link. This data item is a pointer to _chem_comp.type in the CHEM_COMP category.
Mandatory: yes
The type of the second of the two components joined by the link. This data item is a pointer to _chem_comp.type in the CHEM_COMP category.
Data items in the CHEM_COMP_PLANE category provide identifiers for the planes in a chemical component. The atoms in the plane are specified in the CHEM_COMP_PLANE_ATOM category.
Mandatory: no
Keys: _chem_comp_plane.comp_id _chem_comp_plane.id
Groups: inclusive_group chem_comp_group
Examples:
| Example | Detail |
|---|---|
loop_
_chem_comp_plane.comp_id
_chem_comp_plane.id
phe phe1
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
| Name | Category | Mandatory |
|---|---|---|
| _chem_comp_plane.id | chem_comp_plane | yes |
| _chem_comp_plane_atom.plane_id | chem_comp_plane_atom | yes |
The value of _chem_comp_plane.id must uniquely identify a record in the CHEM_COMP_PLANE list.
Type: code
Child / Parent relations:
| Child | Parent |
|---|---|
| _chem_comp_plane_atom.plane_id | _chem_comp_plane.id |
Mandatory: yes
This data item is a pointer to _chem_comp.id in the CHEM_COMP category.
Category: chem_comp_plane
Mandatory: no
The total number of atoms in the plane.
Type: int
Category: chem_comp_plane
Mandatory: no
The number of non-hydrogen atoms in the plane.
Type: int
Data items in the CHEM_COMP_PLANE_ATOM category enumerate the atoms in a plane within a chemical component.
Mandatory: no
Keys: _chem_comp_plane_atom.plane_id _chem_comp_plane_atom.atom_id _chem_comp_plane_atom.comp_id
Groups: inclusive_group chem_comp_group
Examples:
| Example | Detail |
|---|---|
loop_
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.atom_id
phe1 phe CB
phe1 phe CG
phe1 phe CD1
phe1 phe CE1
phe1 phe CZ
phe1 phe CE2
phe1 phe CD2
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
Mandatory: yes
The ID of an atom involved in the plane. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category.
Mandatory: yes
This data item is a pointer to _chem_comp.id in the CHEM_COMP category.
Mandatory: yes
This data item is a pointer to _chem_comp_plane.id in the CHEM_COMP_PLANE category.
Mandatory: no
This data item is the standard deviation of the out-of-plane distance for this atom.
Type: float
Units: angstroms
Data items in the CHEM_COMP_TOR category record details about the torsion angles in a chemical component. As torsion angles can have more than one target value, the target values are specified in the CHEM_COMP_TOR_VALUE category.
Mandatory: no
Keys: _chem_comp_tor.comp_id _chem_comp_tor.id
Groups: inclusive_group chem_comp_group
Examples:
| Example | Detail |
|---|---|
loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
phe phe_chi1 N CA CB CG
phe phe_chi2 CA CB CG CD1
phe phe_ring1 CB CG CD1 CE1
phe phe_ring2 CB CG CD2 CE2
phe phe_ring3 CG CD1 CE1 CZ
phe phe_ring4 CD1 CE1 CZ CE2
phe phe_ring5 CE1 CZ CE2 CD2
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
Mandatory: yes
The ID of the first of the four atoms that define the torsion angle. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category.
Dependent items: _chem_comp_tor.atom_id_2 _chem_comp_tor.atom_id_3 _chem_comp_tor.atom_id_4
Mandatory: yes
The ID of the second of the four atoms that define the torsion angle. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category.
Dependent items: _chem_comp_tor.atom_id_1 _chem_comp_tor.atom_id_3 _chem_comp_tor.atom_id_4
Mandatory: yes
The ID of the third of the four atoms that define the torsion angle. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category.
Dependent items: _chem_comp_tor.atom_id_1 _chem_comp_tor.atom_id_2 _chem_comp_tor.atom_id_4
Mandatory: yes
The ID of the fourth of the four atoms that define the torsion angle. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category.
Dependent items: _chem_comp_tor.atom_id_1 _chem_comp_tor.atom_id_2 _chem_comp_tor.atom_id_3
| Name | Category | Mandatory |
|---|---|---|
| _chem_comp_tor.id | chem_comp_tor | yes |
| _chem_comp_tor_value.tor_id | chem_comp_tor_value | yes |
The value of _chem_comp_tor.id must uniquely identify a record in the CHEM_COMP_TOR list.
Type: code
Child / Parent relations:
| Child | Parent |
|---|---|
| _chem_comp_tor_value.tor_id | _chem_comp_tor.id |
Mandatory: yes
This data item is a pointer to _chem_comp.id in the CHEM_COMP category.
Data items in the CHEM_COMP_TOR_VALUE category record details about the target values for the torsion angles enumerated in the CHEM_COMP_TOR list. Target values may be specified as angles in degrees, as a distance between the first and fourth atoms, or both.
Mandatory: no
Keys: _chem_comp_tor_value.tor_id _chem_comp_tor_value.comp_id
Groups: inclusive_group chem_comp_group
Examples:
| Example | Detail |
|---|---|
loop_
_chem_comp_tor_value.tor_id
_chem_comp_tor_value.comp_id
_chem_comp_tor_value.angle
_chem_comp_tor_value.dist
phe_chi1 phe -60.0 2.88
phe_chi1 phe 180.0 3.72
phe_chi1 phe 60.0 2.88
phe_chi2 phe 90.0 3.34
phe_chi2 phe -90.0 3.34
phe_ring1 phe 180.0 3.75
phe_ring2 phe 180.0 3.75
phe_ring3 phe 0.0 2.80
phe_ring4 phe 0.0 2.80
phe_ring5 phe 0.0 2.80
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
Mandatory: yes
This data item is a pointer to _chem_comp_atom.comp_id in the CHEM_COMP_ATOM category.
Mandatory: yes
This data item is a pointer to _chem_comp_tor.id in the CHEM_COMP_TOR category.
Category: chem_comp_tor_value
Mandatory: yes
A value that should be taken as a potential target value for the torsion angle associated with the specified atoms, expressed in degrees.
Type: float
Type conditions: esd
Units: degrees
Related item: _chem_comp_tor_value.angle_esd (associated_esd)
Range: [180.0, 180.0] [-180.0, 180.0] [-180.0, -180.0]
Category: chem_comp_tor_value
Mandatory: yes
The standard uncertainty (estimated standard deviation) of _chem_comp_tor_value.angle.
Type: float
Units: degrees
Related item: _chem_comp_tor_value.angle (associated_value)
Range: [180.0, 180.0] [-180.0, 180.0] [-180.0, -180.0]
Category: chem_comp_tor_value
Mandatory: no
A value that should be taken as a potential target value for the torsion angle associated with the specified atoms, expressed as the distance between the atoms specified by _chem_comp_tor.atom_id_1 and _chem_comp_tor.atom_id_4 in the referenced record in the CHEM_COMP_TOR list. Note that the torsion angle cannot be fully specified by a distance (for instance, a torsion angle of -60 degree will yield the same distance as a 60 degree angle). However, the distance specification can be useful for refinement in situations in which the angle is already close to the desired value.
Type: float
Type conditions: esd
Units: angstroms
Related item: _chem_comp_tor_value.dist_esd (associated_esd)
Range: [0.0, .] [0.0, 0.0]
Category: chem_comp_tor_value
Mandatory: no
The standard uncertainty (estimated standard deviation) of _chem_comp_tor_value.dist.
Type: float
Units: angstroms
Related item: _chem_comp_tor_value.dist (associated_value)
Range: [0.0, .] [0.0, 0.0]
Data items in the CHEM_LINK category give details about the links between chemical components.
Mandatory: no
Keys: _chem_link.id
Groups: inclusive_group chem_link_group
| Name | Category | Mandatory |
|---|---|---|
| _chem_link.id | chem_link | yes |
| _chem_link_angle.link_id | chem_link_angle | yes |
| _chem_link_bond.link_id | chem_link_bond | yes |
| _chem_link_chir.link_id | chem_link_chir | yes |
| _chem_link_plane.link_id | chem_link_plane | yes |
| _chem_link_tor.link_id | chem_link_tor | yes |
| _chem_comp_link.link_id | chem_comp_link | yes |
| _entity_link.link_id | entity_link | yes |
The value of _chem_link.id must uniquely identify each item in the CHEM_LINK list.
Type: code
Child / Parent relations:
Examples:
| Example | Detail |
|---|---|
peptide |
|
oligosaccharide 1,4 |
|
DNA |
Category: chem_link
Mandatory: no
A description of special aspects of a link between chemical components in the structure.
Type: text
Data items in the CHEM_LINK_ANGLE category record details about angles in a link between chemical components.
Mandatory: no
Keys: _chem_link_angle.link_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_id_2 _chem_link_angle.atom_id_3
Groups: inclusive_group chem_link_group
Examples:
| Example | Detail |
|---|---|
loop_
_chem_link_angle.link_id
_chem_link_angle.value_angle
_chem_link_angle.value_angle_esd
_chem_link_angle.atom_id_1
_chem_link_angle.atom_1_comp_id
_chem_link_angle.atom_id_2
_chem_link_angle.atom_2_comp_id
_chem_link_angle.atom_id_3
_chem_link_angle.atom_3_comp_id
PEPTIDE 111.2 2.8 N 1 CA 1 C 1
PEPTIDE 120.8 1.7 CA 1 C 1 O 1
PEPTIDE 116.2 2.0 CA 1 C 1 N 2
PEPTIDE 123.0 1.6 O 1 C 1 N 2
PEPTIDE 121.7 1.8 C 1 N 2 CA 2
|
Example 1 - Engh & Huber parameters [Acta Cryst. (1991), A47, 392-400] as interpreted by J. P. Priestle (1995). Consistent Stereochemical Dictionaries for Refinement and Model Building. CCP4 Daresbury Study Weekend, DL-CONF-95-001, ISSN 1358-6254. Warrington: Daresbury Laboratory. |
Category: chem_link_angle
Mandatory: no
This data item indicates whether atom 1 is found in the first or the second of the two components connected by the link.
Type: ucode
Dependent items: _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_3_comp_id
Enumeration values:
| Value | Detail |
|---|---|
1 |
the atom is in component 1 |
2 |
the atom is in component 2 |
Category: chem_link_angle
Mandatory: no
This data item indicates whether atom 2 is found in the first or the second of the two components connected by the link.
Type: ucode
Dependent items: _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_3_comp_id
Enumeration values:
| Value | Detail |
|---|---|
1 |
the atom is in component 1 |
2 |
the atom is in component 2 |
Category: chem_link_angle
Mandatory: no
This data item indicates whether atom 3 is found in the first or the second of the two components connected by the link.
Type: ucode
Dependent items: _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_2_comp_id
Enumeration values:
| Value | Detail |
|---|---|
1 |
the atom is in component 1 |
2 |
the atom is in component 2 |
Category: chem_link_angle
Mandatory: yes
The ID of the first of the three atoms that define the angle. An atom with this ID must exist in the component of the type specified by _chem_comp_link.type_comp_1 (or _chem_comp_link.type_comp_2, where the appropriate data item is indicated by the value of _chem_comp_angle.atom_1_comp_id).
Type: code
Dependent items: _chem_link_angle.atom_id_2 _chem_link_angle.atom_id_3
Category: chem_link_angle
Mandatory: yes
The ID of the second of the three atoms that define the angle. The second atom is taken to be the apex of the angle. An atom with this ID must exist in the component of the type specified by _chem_comp_link.type_comp_1 (or _chem_comp_link.type_comp_2, where the appropriate data item is indicated by the value of _chem_comp_angle.atom_2_comp_id).
Type: code
Dependent items: _chem_link_angle.atom_id_1 _chem_link_angle.atom_id_3
Category: chem_link_angle
Mandatory: yes
The ID of the third of the three atoms that define the angle. An atom with this ID must exist in the component of the type specified by _chem_comp_link.type_comp_1 (or _chem_comp_link.type_comp_2, where the appropriate data item is indicated by the value of _chem_comp_angle.atom_3_comp_id).
Type: code
Dependent items: _chem_link_angle.atom_id_1 _chem_link_angle.atom_id_2
Mandatory: yes
This data item is a pointer to _chem_link.id in the CHEM_LINK category.
Category: chem_link_angle
Mandatory: no
The value that should be taken as the target value for the angle associated with the specified atoms, expressed in degrees.
Type: float
Type conditions: esd
Units: degrees
Related item: _chem_link_angle.value_angle_esd (associated_esd)
Range: [180.0, 180.0] [0.0, 180.0] [0.0, 0.0]
Category: chem_link_angle
Mandatory: no
The standard uncertainty (estimated standard deviation) of _chem_link_angle.value_angle.
Type: float
Units: degrees
Related item: _chem_link_angle.value_angle (associated_value)
Range: [180.0, 180.0] [0.0, 180.0] [0.0, 0.0]
Category: chem_link_angle
Mandatory: no
The value that should be taken as the target value for the angle associated with the specified atoms, expressed as the distance between the atoms specified by _chem_comp_angle.atom_id_1 and _chem_comp_angle.atom_id_3.
Type: float
Type conditions: esd
Units: angstroms
Related item: _chem_link_angle.value_dist_esd (associated_esd)
Range: [0.0, .] [0.0, 0.0]
Category: chem_link_angle
Mandatory: no
The standard uncertainty (estimated standard deviation) of _chem_comp_angle.value_dist.
Type: float
Units: angstroms
Related item: _chem_link_angle.value_dist (associated_value)
Range: [0.0, .] [0.0, 0.0]
Data items in the CHEM_LINK_BOND category record details about bonds in a link between components in the chemical structure.
Mandatory: no
Keys: _chem_link_bond.link_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_id_2
Groups: inclusive_group chem_link_group
Examples:
| Example | Detail |
|---|---|
loop_
_chem_link_bond.link_id
_chem_link_bond.value_dist
_chem_link_bond.value_dist_esd
_chem_link_bond.atom_id_1
_chem_link_bond.atom_1_comp_id
_chem_link_bond.atom_id_2
_chem_link_bond.atom_2_comp_id
PEPTIDE 1.458 0.019 N 1 CA 1
PEPTIDE 1.525 0.021 CA 1 C 1
PEPTIDE 1.329 0.014 C 1 N 2
PEPTIDE 1.231 0.020 C 1 O 1
|
Example 1 - Engh & Huber parameters [Acta Cryst. (1991), A47, 392-400] as interpreted by J. P. Priestle (1995). Consistent Stereochemical Dictionaries for Refinement and Model Building. CCP4 Daresbury Study Weekend, DL-CONF-95-001, ISSN 1358-6254. Warrington: Daresbury Laboratory. |
Category: chem_link_bond
Mandatory: no
This data item indicates whether atom 1 is found in the first or the second of the two components connected by the link.
Type: ucode
Dependent items: _chem_link_bond.atom_2_comp_id
Enumeration values:
| Value | Detail |
|---|---|
1 |
the atom is in component 1 |
2 |
the atom is in component 2 |
Category: chem_link_bond
Mandatory: no
This data item indicates whether atom 2 is found in the first or the second of the two chemical components connected by the link.
Type: ucode
Dependent item: _chem_link_bond.atom_1_comp_id
Enumeration values:
| Value | Detail |
|---|---|
1 |
the atom is in component 1 |
2 |
the atom is in component 2 |
Category: chem_link_bond
Mandatory: yes
The ID of the first of the two atoms that define the bond. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense.
Type: code
Dependent items: _chem_link_bond.atom_id_2
Category: chem_link_bond
Mandatory: yes
The ID of the second of the two atoms that define the bond. As this data item does not point to a specific atom in a specific component, it is not a child in the linkage sense.
Type: code
Dependent item: _chem_link_bond.atom_id_1
Mandatory: yes
This data item is a pointer to _chem_link.id in the CHEM_LINK category.
Category: chem_link_bond
Mandatory: no
The value that should be taken as the target for the chemical bond associated with the specified atoms, expressed as a distance.
Type: float
Type conditions: esd
Units: angstroms
Related item: _chem_link_bond.value_dist_esd (associated_esd)
Range: [0.0, .] [0.0, 0.0]
Category: chem_link_bond
Mandatory: no
The standard uncertainty (estimated standard deviation) of _chem_link_bond.value_dist.
Type: float
Units: angstroms
Related item: _chem_link_bond.value_dist (associated_value)
Range: [0.0, .] [0.0, 0.0]
Category: chem_link_bond
Mandatory: no
The value that should be taken as the target for the chemical bond associated with the specified atoms, expressed as a bond order.
Type: ucode
Default value: sing
Enumeration values:
| Value | Detail |
|---|---|
sing |
single bond |
doub |
double bond |
trip |
triple bond |
quad |
quadruple bond |
arom |
aromatic bond |
poly |
polymeric bond |
delo |
delocalized double bond |
pi |
pi bond |
Data items in the CHEM_LINK_CHIR category provide details about the chiral centres in a link between two chemical components. The atoms bonded to the chiral atom are specified in the CHEM_LINK_CHIR_ATOM category.
Mandatory: no
Keys: _chem_link_chir.link_id _chem_link_chir.id
Groups: inclusive_group chem_link_group
Category: chem_link_chir
Mandatory: no
This data item indicates whether the chiral atom is found in the first or the second of the two components connected by the link.
Type: ucode
Enumeration values:
| Value | Detail |
|---|---|
1 |
the atom is in component 1 |
2 |
the atom is in component 2 |
Mandatory: yes
The ID of the atom that is a chiral centre. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense.
Type: code
Category: chem_link_chir
Mandatory: no
The chiral configuration of the atom that is a chiral centre.
Type: ucode
Enumeration values:
| Value | Detail |
|---|---|
R |
absolute configuration R |
S |
absolute configuration S |
| Name | Category | Mandatory |
|---|---|---|
| _chem_link_chir.id | chem_link_chir | yes |
| _chem_link_chir_atom.chir_id | chem_link_chir_atom | yes |
The value of _chem_link_chir.id must uniquely identify a record in the CHEM_LINK_CHIR list.
Type: code
Child / Parent relations:
| Child | Parent |
|---|---|
| _chem_link_chir_atom.chir_id | _chem_link_chir.id |
Mandatory: yes
This data item is a pointer to _chem_link.id in the CHEM_LINK category.
Category: chem_link_chir
Mandatory: no
The total number of atoms bonded to the atom specified by _chem_link_chir.atom_id.
Type: int
Category: chem_link_chir
Mandatory: no
The number of non-hydrogen atoms bonded to the atom specified by _chem_link_chir.atom_id.
Type: int
Category: chem_link_chir
Mandatory: no
A flag to indicate whether a chiral volume should match the standard value in both magnitude and sign, or in magnitude only.
Type: ucode
Enumeration values:
| Value | Detail |
|---|---|
sign |
match magnitude and sign |
nosign |
match magnitude only |
Category: chem_link_chir
Mandatory: no
The chiral volume, V(c), for chiral centres that involve a chiral atom bonded to three non-hydrogen atoms and one hydrogen atom. Vc = V1 * (V2 X V3) V1 = the vector distance from the atom specified by _chem_link_chir.atom_id to the first atom in the CHEM_LINK_CHIR_ATOM list V2 = the vector distance from the atom specified by _chem_link_chir.atom_id to the second atom in the CHEM_LINK_CHIR_ATOM list V3 = the vector distance from the atom specified by _chem_link_chir.atom_id to the third atom in the CHEM_LINK_CHIR_ATOM list * = the vector dot product X = the vector cross product
Type: float
Type conditions: esd
Units: angstroms_cubed
Related item: _chem_link_chir.volume_three_esd (associated_esd)
Category: chem_link_chir
Mandatory: no
The standard uncertainty (estimated standard deviation) of _chem_link_chir.volume_three.
Type: float
Units: angstroms_cubed
Related item: _chem_link_chir.volume_three (associated_value)
Data items in the CHEM_LINK_CHIR_ATOM category enumerate the atoms bonded to a chiral atom in a link between two chemical components.
Mandatory: no
Keys: _chem_link_chir_atom.chir_id _chem_link_chir_atom.atom_id
Groups: inclusive_group chem_link_group
Category: chem_link_chir_atom
Mandatory: no
This data item indicates whether the atom bonded to a chiral atom is found in the first or the second of the two components connected by the link.
Type: ucode
Enumeration values:
| Value | Detail |
|---|---|
1 |
the atom is in component 1 |
2 |
the atom is in component 2 |
Mandatory: yes
The ID of an atom bonded to the chiral atom. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense.
Type: code
Mandatory: yes
This data item is a pointer to _chem_link_chir.id in the CHEM_LINK_CHIR category.
Category: chem_link_chir_atom
Mandatory: no
The standard uncertainty (estimated standard deviation) of the position of this atom from the plane defined by all of the atoms in the plane.
Type: float
Units: angstroms
Data items in the CHEM_LINK_PLANE category provide identifiers for the planes in a link between two chemical components. The atoms in the plane are specified in the CHEM_LINK_PLANE_ATOM category.
Mandatory: no
Keys: _chem_link_plane.link_id _chem_link_plane.id
Groups: inclusive_group chem_link_group
| Name | Category | Mandatory |
|---|---|---|
| _chem_link_plane.id | chem_link_plane | yes |
| _chem_link_plane_atom.plane_id | chem_link_plane_atom | yes |
The value of _chem_link_plane.id must uniquely identify a record in the CHEM_LINK_PLANE list.
Type: code
Child / Parent relations:
| Child | Parent |
|---|---|
| _chem_link_plane_atom.plane_id | _chem_link_plane.id |
Mandatory: yes
This data item is a pointer to _chem_link.id in the CHEM_LINK category.
Category: chem_link_plane
Mandatory: no
The total number of atoms in the plane.
Type: int
Category: chem_link_plane
Mandatory: no
The number of non-hydrogen atoms in the plane.
Type: int
Data items in the CHEM_LINK_PLANE_ATOM category enumerate the atoms in a plane in a link between two chemical components.
Mandatory: no
Keys: _chem_link_plane_atom.plane_id _chem_link_plane_atom.atom_id
Groups: inclusive_group chem_link_group
Category: chem_link_plane_atom
Mandatory: no
This data item indicates whether the atom in a plane is found in the first or the second of the two components connected by the link.
Type: ucode
Enumeration values:
| Value | Detail |
|---|---|
1 |
the atom is in component 1 |
2 |
the atom is in component 2 |
Mandatory: yes
The ID of an atom involved in the plane. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense.
Type: code
Mandatory: yes
This data item is a pointer to _chem_link_plane.id in the CHEM_LINK_PLANE category.
Data items in the CHEM_LINK_TOR category record details about the torsion angles in a link between two chemical components. As torsion angles can have more than one target value, the target values are specified in the CHEM_LINK_TOR_VALUE category.
Mandatory: no
Keys: _chem_link_tor.link_id _chem_link_tor.id
Groups: inclusive_group chem_link_group
Category: chem_link_tor
Mandatory: no
This data item indicates whether atom 1 is found in the first or the second of the two components connected by the link.
Type: ucode
Dependent items: _chem_link_tor.atom_2_comp_id _chem_link_tor.atom_3_comp_id _chem_link_tor.atom_4_comp_id
Enumeration values:
| Value | Detail |
|---|---|
1 |
the atom is in component 1 |
2 |
the atom is in component 2 |
Category: chem_link_tor
Mandatory: no
This data item indicates whether atom 2 is found in the first or the second of the two components connected by the link.
Type: ucode
Dependent items: _chem_link_tor.atom_1_comp_id _chem_link_tor.atom_3_comp_id _chem_link_tor.atom_4_comp_id
Enumeration values:
| Value | Detail |
|---|---|
1 |
the atom is in component 1 |
2 |
the atom is in component 2 |
Category: chem_link_tor
Mandatory: no
This data item indicates whether atom 3 is found in the first or the second of the two components connected by the link.
Type: ucode
Dependent items: _chem_link_tor.atom_1_comp_id _chem_link_tor.atom_2_comp_id _chem_link_tor.atom_4_comp_id
Enumeration values:
| Value | Detail |
|---|---|
1 |
the atom is in component 1 |
2 |
the atom is in component 2 |
Category: chem_link_tor
Mandatory: no
This data item indicates whether atom 4 is found in the first or the second of the two components connected by the link.
Type: ucode
Dependent items: _chem_link_tor.atom_1_comp_id _chem_link_tor.atom_2_comp_id _chem_link_tor.atom_3_comp_id
Enumeration values:
| Value | Detail |
|---|---|
1 |
the atom is in component 1 |
2 |
the atom is in component 2 |
Mandatory: yes
The ID of the first of the four atoms that define the torsion angle. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense.
Type: code
Dependent items: _chem_link_tor.atom_id_2 _chem_link_tor.atom_id_3 _chem_link_tor.atom_id_4
Mandatory: yes
The ID of the second of the four atoms that define the torsion angle. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense.
Type: code
Dependent items: _chem_link_tor.atom_id_1 _chem_link_tor.atom_id_3 _chem_link_tor.atom_id_4
Mandatory: yes
The ID of the third of the four atoms that define the torsion angle. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense.
Type: code
Dependent items: _chem_link_tor.atom_id_1 _chem_link_tor.atom_id_2 _chem_link_tor.atom_id_4
Mandatory: yes
The ID of the fourth of the four atoms that define the torsion angle. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense.
Type: code
Dependent items: _chem_link_tor.atom_id_1 _chem_link_tor.atom_id_2 _chem_link_tor.atom_id_3
| Name | Category | Mandatory |
|---|---|---|
| _chem_link_tor.id | chem_link_tor | yes |
| _chem_link_tor_value.tor_id | chem_link_tor_value | yes |
The value of _chem_link_tor.id must uniquely identify a record in the CHEM_LINK_TOR list.
Type: code
Child / Parent relations:
| Child | Parent |
|---|---|
| _chem_link_tor_value.tor_id | _chem_link_tor.id |
Mandatory: yes
This data item is a pointer to _chem_link.id in the CHEM_LINK category.
Data items in the CHEM_LINK_TOR_VALUE category record details about the target values for the torsion angles enumerated in the CHEM_LINK_TOR list. Target values may be specified as angles in degrees, as a distance between the first and fourth atoms, or both.
Mandatory: no
Keys: _chem_link_tor_value.tor_id
Groups: inclusive_group chem_link_group
Mandatory: yes
This data item is a pointer to _chem_link_tor.id in the CHEM_LINK_TOR category.
Category: chem_link_tor_value
Mandatory: yes
A value that should be taken as a potential target value for the torsion angle associated with the specified atoms, expressed in degrees.
Type: float
Type conditions: esd
Units: degrees
Related item: _chem_link_tor_value.angle_esd (associated_esd)
Range: [180.0, 180.0] [-180.0, 180.0] [-180.0, -180.0]
Category: chem_link_tor_value
Mandatory: yes
The standard uncertainty (estimated standard deviation) of _chem_link_tor_value.angle.
Type: float
Units: degrees
Related item: _chem_link_tor_value.angle (associated_value)
Range: [180.0, 180.0] [-180.0, 180.0] [-180.0, -180.0]
Category: chem_link_tor_value
Mandatory: no
A value that should be taken as a potential target value for the torsion angle associated with the specified atoms, expressed as the distance between the atoms specified by _chem_link_tor.atom_id_1 and _chem_link_tor.atom_id_4 in the referenced record in the CHEM_LINK_TOR list. Note that the torsion angle cannot be fully specified by a distance (for instance, a torsion angle of -60 degree will yield the same distance as a 60 degree angle). However, the distance specification can be useful for refinement in situations in which the angle is already close to the desired value.
Type: float
Type conditions: esd
Units: angstroms
Related item: _chem_link_tor_value.dist_esd (associated_esd)
Range: [0.0, .] [0.0, 0.0]
Category: chem_link_tor_value
Mandatory: no
The standard uncertainty (estimated standard deviation) of _chem_link_tor_value.dist.
Type: float
Units: angstroms
Related item: _chem_link_tor_value.dist (associated_value)
Range: [0.0, .] [0.0, 0.0]
Data items in the CHEMICAL category would not in general be used in a macromolecular CIF. See instead the ENTITY data items. Data items in the CHEMICAL category record details about the composition and chemical properties of the compounds. The formula data items must agree with those that specify the density, unit-cell and Z values.
Mandatory: no
Keys: _chemical.entry_id
Groups: inclusive_group chemical_group
Examples:
| Example | Detail |
|---|---|
_chemical.entry_id '9597gaus'
_chemical.name_systematic
trans-bis(tricyclohexylphosphine)tetracarbonylmolybdenum(0)
|
Example 1 - based on data set 9597gaus of Alyea, Ferguson & Kannan [Acta Cryst. (1996), C52, 765-767]. |
Mandatory: yes
This data item is a pointer to _entry.id in the ENTRY category.
Category: chemical
Mandatory: no
Description of the source of the compound under study, or of the parent molecule if a simple derivative is studied. This includes the place of discovery for minerals or the actual source of a natural product.
Alias: _chemical_compound_source (cif_core.dic, 2.0.1)
Type: text
Examples:
| Example | Detail |
|---|---|
From Norilsk (USSR) |
|
Extracted from the bark of Cinchona Naturalis |
Category: chemical
Mandatory: no
The temperature in kelvins at which the crystalline solid changes to a liquid.
Alias: _chemical_melting_point (cif_core.dic, 2.0.1)
Type: float
Units: kelvins
Range: [0.0, .] [0.0, 0.0]
Category: chemical
Mandatory: no
Trivial name by which the compound is commonly known.
Alias: _chemical_name_common (cif_core.dic, 2.0.1)
Type: text
Example:
1-bromoestradiol
Category: chemical
Mandatory: no
Mineral name accepted by the International Mineralogical Association. Use only for natural minerals. See also _chemical.compound_source.
Alias: _chemical_name_mineral (cif_core.dic, 2.0.1)
Type: text
Example:
chalcopyrite
Category: chemical
Mandatory: no
Commonly used structure-type name. Usually only applied to minerals or inorganic compounds.
Alias: _chemical_name_structure_type (cif_core.dic, 2.0.1)
Type: text
Examples:
| Example | Detail |
|---|---|
perovskite |
|
sphalerite |
|
A15 |
Category: chemical
Mandatory: no
IUPAC or Chemical Abstracts full name of the compound.
Alias: _chemical_name_systematic (cif_core.dic, 2.0.1)
Type: text
Example:
1-bromoestra-1,3,5(10)-triene-3,17\b-diol
Data items in the CHEMICAL_CONN_ATOM category would not, in general, be used in a macromolecular CIF. See instead the ENTITY data items. Data items in the CHEMICAL_CONN_ATOM and CHEMICAL_CONN_BOND categories record details about the two-dimensional (2D) chemical structure of the molecular species. They allow a 2D chemical diagram to be reconstructed for use in a publication or in a database search for structural and substructural relationships. The CHEMICAL_CONN_ATOM data items provide information about the chemical properties of the atoms in the structure. In cases where crystallographic and molecular symmetry elements coincide, they must also contain symmetry-generated atoms, so that the CHEMICAL_CONN_ATOM and CHEMICAL_CONN_BOND data items will always describe a complete chemical entity.
Mandatory: no
Keys: _chemical_conn_atom.number
Groups: inclusive_group chemical_group
Examples:
| Example | Detail |
|---|---|
loop_
_chemical_conn_atom.number
_chemical_conn_atom.type_symbol
_chemical_conn_atom.display_x
_chemical_conn_atom.display_y
_chemical_conn_atom.NCA
_chemical_conn_atom.NH
1 S .39 .81 1 0
2 S .39 .96 2 0
3 N .14 .88 3 0
4 C .33 .88 3 0
5 C .11 .96 2 2
6 C .03 .96 2 2
7 C .03 .80 2 2
8 C .11 .80 2 2
9 S .54 .81 1 0
10 S .54 .96 2 0
11 N .80 .88 3 0
12 C .60 .88 3 0
13 C .84 .96 2 2
14 C .91 .96 2 2
15 C .91 .80 2 2
16 C .84 .80 2 2
|
Example 1 - based on data set DPTD of Yamin, Suwandi, Fun, Sivakumar & bin Shawkataly [Acta Cryst. (1996), C52, 951-953]. |
Category: chemical_conn_atom
Mandatory: no
The net integer charge assigned to this atom. This is the formal charge assignment normally found in chemical diagrams.
Alias: _chemical_conn_atom_charge (cif_core.dic, 2.0.1)
Type: int
Default value: 0
Range: [8, 8] [-8, 8] [-8, -8]
Examples:
| Example | Detail |
|---|---|
1 |
for an ammonium nitrogen |
-1 |
for a chloride ion |
Category: chemical_conn_atom
Mandatory: no
The 2D Cartesian x coordinate of the position of this atom in a recognizable chemical diagram. The coordinate origin is at the lower left corner, the x axis is horizontal and the y axis is vertical. The coordinates must lie in the range 0.0 to 1.0. These coordinates can be obtained from projections of a suitable uncluttered view of the molecular structure.
Alias: _chemical_conn_atom_display_x (cif_core.dic, 2.0.1)
Type: float
Dependent item: _chemical_conn_atom.display_y
Range: [1.0, 1.0] [0.0, 1.0] [0.0, 0.0]
Category: chemical_conn_atom
Mandatory: no
The 2D Cartesian y coordinate of the position of this atom in a recognizable chemical diagram. The coordinate origin is at the lower left corner, the x axis is horizontal and the y axis is vertical. The coordinates must lie in the range 0.0 to 1.0. These coordinates can be obtained from projections of a suitable uncluttered view of the molecular structure.
Alias: _chemical_conn_atom_display_y (cif_core.dic, 2.0.1)
Type: float
Dependent item: _chemical_conn_atom.display_x
Range: [1.0, 1.0] [0.0, 1.0] [0.0, 0.0]
Category: chemical_conn_atom
Mandatory: no
The number of connected atoms excluding terminal hydrogen atoms.
Alias: _chemical_conn_atom_NCA (cif_core.dic, 2.0.1)
Type: int
Range: [0, .] [0, 0]
Category: chemical_conn_atom
Mandatory: no
The total number of hydrogen atoms attached to this atom, regardless of whether they are included in the refinement or the ATOM_SITE list. This number is the same as _atom_site.attached_hydrogens only if none of the hydrogen atoms appear in the ATOM_SITE list.
Alias: _chemical_conn_atom_NH (cif_core.dic, 2.0.1)
Type: int
Range: [0, .] [0, 0]
| Name | Category | Mandatory |
|---|---|---|
| _chemical_conn_atom.number | chemical_conn_atom | yes |
| _atom_site.chemical_conn_number | atom_site | no |
| _chemical_conn_bond.atom_1 | chemical_conn_bond | yes |
| _chemical_conn_bond.atom_2 | chemical_conn_bond | yes |
The chemical sequence number to be associated with this atom. Within an ATOM_SITE list, this number must match one of the _atom_site.chemical_conn_number values.
Alias: _chemical_conn_atom_number (cif_core.dic, 2.0.1)
Type: int
Child / Parent relations:
| Child | Parent |
|---|---|
| _atom_site.chemical_conn_number | _chemical_conn_atom.number |
| _chemical_conn_bond.atom_1 | _chemical_conn_atom.number |
| _chemical_conn_bond.atom_2 | _chemical_conn_atom.number |
Range: [1, .] [1, 1]
Mandatory: yes
This data item is a pointer to _atom_type.symbol in the ATOM_TYPE category.
Alias: _chemical_conn_atom_type_symbol (cif_core.dic, 2.0.1)
Data items in the CHEMICAL_CONN_BOND category would not, in general, be used in a macromolecular CIF. See instead the ENTITY data items. Data items in the CHEMICAL_CONN_ATOM and CHEMICAL_CONN_BOND categories record details about the two-dimensional (2D) chemical structure of the molecular species. They allow a 2D chemical diagram to be reconstructed for use in a publication or in a database search for structural and substructural relationships. The CHEMICAL_CONN_BOND data items specify the connections between the atoms in the CHEMICAL_CONN_ATOM list and the nature of the chemical bond between these atoms.
Mandatory: no
Keys: _chemical_conn_bond.atom_1 _chemical_conn_bond.atom_2
Groups: inclusive_group chemical_group
Examples:
| Example | Detail |
|---|---|
loop_
_chemical_conn_bond.atom_1
_chemical_conn_bond.atom_2
_chemical_conn_bond.type
4 1 doub 4 3 sing
4 2 sing 5 3 sing
6 5 sing 7 6 sing
8 7 sing 8 3 sing
10 2 sing 12 9 doub
12 11 sing 12 10 sing
13 11 sing 14 13 sing
15 14 sing 16 15 sing
16 11 sing 17 5 sing
18 5 sing 19 6 sing
20 6 sing 21 7 sing
22 7 sing 23 8 sing
24 8 sing 25 13 sing
26 13 sing 27 14 sing
28 14 sing 29 15 sing
30 15 sing 31 16 sing
32 16 sing
|
Example 1 - based on data set DPTD of Yamin, Suwandi, Fun, Sivakumar & bin Shawkataly [Acta Cryst. (1996), C52, 951-953]. |
Mandatory: yes
This data item is a pointer to _chemical_conn_atom.number in the CHEMICAL_CONN_ATOM category.
Alias: _chemical_conn_bond_atom_1 (cif_core.dic, 2.0.1)
Dependent item: _chemical_conn_bond.atom_2
Mandatory: yes
This data item is a pointer to _chemical_conn_atom.number in the CHEMICAL_CONN_ATOM category.
Alias: _chemical_conn_bond_atom_2 (cif_core.dic, 2.0.1)
Dependent item: _chemical_conn_bond.atom_1
Category: chemical_conn_bond
Mandatory: no
The chemical bond type associated with the connection between the two sites _chemical_conn_bond.atom_1 and _chemical_conn_bond.atom_2.
Alias: _chemical_conn_bond_type (cif_core.dic, 2.0.1)
Type: ucode
Default value: sing
Enumeration values:
| Value | Detail |
|---|---|
sing |
single bond |
doub |
double bond |
trip |
triple bond |
quad |
quadruple bond |
arom |
aromatic bond |
poly |
polymeric bond |
delo |
delocalized double bond |
pi |
pi bond |
Data items in the CHEMICAL_FORMULA category would not, in general, be used in a macromolecular CIF. See instead the ENTITY data items. Data items in the CHEMICAL_FORMULA category specify the composition and chemical properties of the compound. The formula data items must agree with those that specify the density, unit-cell and Z values. The following rules apply to the construction of the data items _chemical_formula.analytical, _chemical_formula.structural and _chemical_formula.sum. For the data item _chemical_formula.moiety, the formula construction is broken up into residues or moieties, i.e. groups of atoms that form a molecular unit or molecular ion. The rules given below apply within each moiety but different requirements apply to the way that moieties are connected (see _chemical_formula.moiety). (1) Only recognized element symbols may be used. (2) Each element symbol is followed by a 'count' number. A count of '1' may be omitted. (3) A space or parenthesis must separate each cluster of (element symbol + count). (4) Where a group of elements is enclosed in parentheses, the multiplier for the group must follow the closing parenthesis. That is, all element and group multipliers are assumed to be printed as subscripted numbers. (An exception to this rule exists for _chemical_formula.moiety formulae where pre- and post-multipliers are permitted for molecular units.) (5) Unless the elements are ordered in a manner that corresponds to their chemical structure, as in _chemical_formula.structural, the order of the elements within any group or moiety should be: C, then H, then the other elements in alphabetical order of their symbol. This is the 'Hill' system used by Chemical Abstracts. This ordering is used in _chemical_formula.moiety and _chemical_formula.sum.
Mandatory: no
Keys: _chemical_formula.entry_id
Groups: inclusive_group chemical_group
Examples:
| Example | Detail |
|---|---|
_chemical_formula.entry_id 'TOZ'
_chemical_formula.moiety 'C18 H25 N O3'
_chemical_formula.sum 'C18 H25 N O3'
_chemical_formula.weight 303.40
|
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. |
Category: chemical_formula
Mandatory: no
Formula determined by standard chemical analysis including trace elements. See the CHEMICAL_FORMULA category description for rules for writing chemical formulae. Parentheses are used only for standard uncertainties (estimated standard deviations).
Alias: _chemical_formula_analytical (cif_core.dic, 2.0.1)
Type: text
Example:
Fe2.45(2) Ni1.60(3) S4
Mandatory: yes
This data item is a pointer to _entry.id in the ENTRY category.
Category: chemical_formula
Mandatory: no
Formula expressed in conformance with IUPAC rules for inorganic and metal-organic compounds where these conflict with the rules for any other CHEMICAL_FORMULA entries. Typically used for formatting a formula in accordance with journal rules. This should appear in the data block in addition to the most appropriate of the other CHEMICAL_FORMULA data names. Ref: IUPAC (1990). Nomenclature of Inorganic Chemistry. Oxford: Blackwell Scientific Publications.
Alias: _chemical_formula_iupac (cif_core.dic, 2.0.1)
Type: text
Example:
[Co Re (C12 H22 P)2 (C O)6].0.5C H3 O H
Category: chemical_formula
Mandatory: no
Formula with each discrete bonded residue or ion shown as a separate moiety. See the CHEMICAL_FORMULA category description for rules for writing chemical formulae. In addition to the general formulae requirements, the following rules apply: (1) Moieties are separated by commas ','. (2) The order of elements within a moiety follows general rule (5) in the CHEMICAL_FORMULA category description. (3) Parentheses are not used within moieties but may surround a moiety. Parentheses may not be nested. (4) Charges should be placed at the end of the moiety. The charge '+' or '-' may be preceded by a numerical multiplier and should be separated from the last (element symbol + count) by a space. Pre- or post-multipliers may be used for individual moieties.
Alias: _chemical_formula_moiety (cif_core.dic, 2.0.1)
Type: text
Examples:
| Example | Detail |
|---|---|
C7 H4 Cl Hg N O3 S |
|
C12 H17 N4 O S 1+, C6 H2 N3 O7 1- |
|
C12 H16 N2 O6, 5(H2 O1) |
|
(Cd 2+)3, (C6 N6 Cr 3-)2, 2(H2 O) |
Category: chemical_formula
Mandatory: no
See the CHEMICAL_FORMULA category description for the rules for writing chemical formulae for inorganics, organometallics, metal complexes etc., in which bonded groups are preserved as discrete entities within parentheses, with post-multipliers as required. The order of the elements should give as much information as possible about the chemical structure. Parentheses may be used and nested as required. This formula should correspond to the structure as actually reported, i.e. trace elements not included in atom-type and atom-site data should not be included in this formula (see also _chemical_formula.analytical).
Alias: _chemical_formula_structural (cif_core.dic, 2.0.1)
Type: text
Examples:
| Example | Detail |
|---|---|
Ca ((Cl O3)2 O)2 (H2 O)6 |
|
(Pt (N H3)2 (C5 H7 N3 O)2) (Cl O4)2 |
Category: chemical_formula
Mandatory: no
See the CHEMICAL_FORMULA category description for the rules for writing chemical formulae in which all discrete bonded residues and ions are summed over the constituent elements, following the ordering given in general rule (5) in the CHEMICAL_FORMULA category description. Parentheses are not normally used.
Alias: _chemical_formula_sum (cif_core.dic, 2.0.1)
Type: text
Examples:
| Example | Detail |
|---|---|
C18 H19 N7 O8 S |
Category: chemical_formula
Mandatory: no
Formula mass in daltons. This mass should correspond to the formulae given under _chemical_formula.structural, _chemical_formula.moiety or _chemical_formula.sum and, together with the Z value and cell parameters, should yield the density given as _exptl_crystal.density_diffrn.
Alias: _chemical_formula_weight (cif_core.dic, 2.0.1)
Type: float
Range: [1.0, .] [1.0, 1.0]
Category: chemical_formula
Mandatory: no
Formula mass in daltons measured by a non-diffraction experiment.
Alias: _chemical_formula_weight_meas (cif_core.dic, 2.0.1)
Type: float
Range: [1.0, .] [1.0, 1.0]
Data items in the CITATION category record details about the literature cited as being relevant to the contents of the data block.
Mandatory: no
Keys: _citation.id
Groups: inclusive_group citation_group
Examples:
| Example | Detail |
|---|---|
loop_
_citation.id
_citation.coordinate_linkage
_citation.title
_citation.country
_citation.journal_abbrev
_citation.journal_volume
_citation.journal_issue
_citation.page_first
_citation.page_last
_citation.year
_citation.journal_id_ASTM
_citation.journal_id_ISSN
_citation.journal_id_CSD
_citation.book_title
_citation.book_publisher
_citation.book_id_ISBN
_citation.details
primary yes
; Crystallographic analysis of a complex between human
immunodeficiency virus type 1 protease and acetyl-pepstatin
at 2.0-Angstroms resolution.
;
US 'J. Biol. Chem.' 265 . 14209 14219 1990
HBCHA3 0021-9258 071 . . .
; The publication that directly relates to this coordinate
set.
;
2 no
; Three-dimensional structure of aspartyl-protease from human
immunodeficiency virus HIV-1.
;
UK 'Nature' 337 . 615 619 1989
NATUAS 0028-0836 006 . . .
; Determination of the structure of the unliganded enzyme.
;
3 no
; Crystallization of the aspartylprotease from human
immunodeficiency virus, HIV-1.
;
US 'J. Biol. Chem.' 264 . 1919 1921 1989
HBCHA3 0021-9258 071 . . .
; Crystallization of the unliganded enzyme.
;
4 no
; Human immunodeficiency virus protease. Bacterial expression
and characterization of the purified aspartic protease.
;
US 'J. Biol. Chem.' 264 . 2307 2312 1989
HBCHA3 0021-9258 071 . . .
; Expression and purification of the enzyme.
;
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
Category: citation
Mandatory: no
Abstract for the citation. This is used most when the citation is extracted from a bibliographic database that contains full text or abstract information.
Alias: _citation_abstract (cif_core.dic, 2.0.1)
Type: text
Category: citation
Mandatory: no
The Chemical Abstracts Service (CAS) abstract identifier; relevant for journal articles.
Alias: _citation_abstract_id_CAS (cif_core.dic, 2.0.1)
Type: text
Category: citation
Mandatory: no
The International Standard Book Number (ISBN) code assigned to the book cited; relevant for books or book chapters.
Alias: _citation_book_id_ISBN (cif_core.dic, 2.0.1)
Type: line
Category: citation
Mandatory: no
The name of the publisher of the citation; relevant for books or book chapters.
Alias: _citation_book_publisher (cif_core.dic, 2.0.1)
Type: text
Example:
John Wiley and Sons
Category: citation
Mandatory: no
The location of the publisher of the citation; relevant for books or book chapters.
Alias: _citation_book_publisher_city (cif_core.dic, 2.0.1)
Type: text
Example:
London
Category: citation
Mandatory: no
The title of the book in which the citation appeared; relevant for books or book chapters.
Alias: _citation_book_title (cif_core.dic, 2.0.1)
Type: text
Category: citation
Mandatory: no
_citation.coordinate_linkage states whether this citation is concerned with precisely the set of coordinates given in the data block. If, for instance, the publication described the same structure, but the coordinates had undergone further refinement prior to the creation of the data block, the value of this data item would be 'no'.
Alias: _citation_coordinate_linkage (cif_core.dic, 2.0.1)
Type: ucode
Enumeration values:
| Value | Detail |
|---|---|
no |
citation unrelated to current coordinates |
n |
abbreviation for "no" |
yes |
citation related to current coordinates |
y |
abbreviation for "yes" |
Category: citation
Mandatory: no
The country of publication; relevant for books and book chapters.
Alias: _citation_country (cif_core.dic, 2.0.1)
Type: line
Category: citation
Mandatory: no
Accession number used by Medline to categorize a specific bibliographic entry.
Alias: _citation_database_id_Medline (cif_core.dic, 2.0.1)
Type: int
Range: [1, .] [1, 1]
Example:
89064067
Category: citation
Mandatory: no
A description of special aspects of the relationship of the contents of the data block to the literature item cited.
Alias: _citation_special_details (cif_core.dic, 2.0.1)
Type: text
Examples:
| Example | Detail |
|---|---|
citation relates to this precise
coordinate set
|
|
citation relates to earlier low-resolution
structure
|
|
citation relates to further refinement of
structure reported in citation 2
|
| Name | Category | Mandatory |
|---|---|---|
| _citation.id | citation | yes |
| _citation_author.citation_id | citation_author | yes |
| _citation_editor.citation_id | citation_editor | yes |
| _software.citation_id | software | no |
The value of _citation.id must uniquely identify a record in the CITATION list. The _citation.id 'primary' should be used to indicate the citation that the author(s) consider to be the most pertinent to the contents of the data block. Note that this item need not be a number; it can be any unique identifier.
Alias: _citation_id (cif_core.dic, 2.0.1)
Type: code
Child / Parent relations:
| Child | Parent |
|---|---|
| _citation_author.citation_id | _citation.id |
| _citation_editor.citation_id | _citation.id |
| _software.citation_id | _citation.id |
Examples:
| Example | Detail |
|---|---|
primary |
|
1 |
|
2 |
Category: citation
Mandatory: no
Abbreviated name of the cited journal as given in the Chemical Abstracts Service Source Index.
Alias: _citation_journal_abbrev (cif_core.dic, 2.0.1)
Type: line
Example:
J. Mol. Biol.
Category: citation
Mandatory: no
The American Society for Testing and Materials (ASTM) code assigned to the journal cited (also referred to as the CODEN designator of the Chemical Abstracts Service); relevant for journal articles.
Alias: _citation_journal_id_ASTM (cif_core.dic, 2.0.1)
Type: line
Category: citation
Mandatory: no
The Cambridge Structural Database (CSD) code assigned to the journal cited; relevant for journal articles. This is also the system used at the Protein Data Bank (PDB).
Alias: _citation_journal_id_CSD (cif_core.dic, 2.0.1)
Type: line
Example:
0070
Category: citation
Mandatory: no
The International Standard Serial Number (ISSN) code assigned to the journal cited; relevant for journal articles.
Alias: _citation_journal_id_ISSN (cif_core.dic, 2.0.1)
Type: line
Category: citation
Mandatory: no
Full name of the cited journal; relevant for journal articles.
Alias: _citation_journal_full (cif_core.dic, 2.0.1)
Type: text
Example:
Journal of Molecular Biology
Category: citation
Mandatory: no
Issue number of the journal cited; relevant for journal articles.
Alias: _citation_journal_issue (cif_core.dic, 2.0.1)
Type: line
Example:
2
Category: citation
Mandatory: no
Volume number of the journal cited; relevant for journal articles.
Alias: _citation_journal_volume (cif_core.dic, 2.0.1)
Type: line
Example:
174
Category: citation
Mandatory: no
Language in which the cited article is written.
Alias: _citation_language (cif_core.dic, 2.0.1)
Type: line
Example:
German
Category: citation
Mandatory: no
The first page of the citation; relevant for journal articles, books and book chapters.
Alias: _citation_page_first (cif_core.dic, 2.0.1)
Type: line
Category: citation
Mandatory: no
The last page of the citation; relevant for journal articles, books and book chapters.
Alias: _citation_page_last (cif_core.dic, 2.0.1)
Type: line
Category: citation
Mandatory: no
The title of the citation; relevant for journal articles, books and book chapters.
Alias: _citation_title (cif_core.dic, 2.0.1)
Type: text
Example:
Structure of diferric duck ovotransferrin
at 2.35 \%A resolution.
Category: citation
Mandatory: no
The year of the citation; relevant for journal articles, books and book chapters.
Alias: _citation_year (cif_core.dic, 2.0.1)
Type: int
Example:
1984
Data items in the CITATION_AUTHOR category record details about the authors associated with the citations in the CITATION list.
Mandatory: no
Keys: _citation_author.citation_id _citation_author.name
Groups: inclusive_group citation_group
Examples:
| Example | Detail |
|---|---|
loop_
_citation_author.citation_id
_citation_author.ordinal
_citation_author.name
primary 1 'Fitzgerald, P.M.D.'
primary 2 'McKeever, B.M.'
primary 3 'Van Middlesworth, J.F.'
primary 4 'Springer, J.P.'
primary 5 'Heimbach, J.C.'
primary 6 'Leu, C.-T.'
primary 7 'Herber, W.K.'
primary 8 'Dixon, R.A.F.'
primary 9 'Darke, P.L.'
2 1 'Navia, M.A.'
2 2 'Fitzgerald, P.M.D.'
2 3 'McKeever, B.M.'
2 4 'Leu, C.-T.'
2 5 'Heimbach, J.C.'
2 6 'Herber, W.K.'
2 7 'Sigal, I.S.'
2 8 'Darke, P.L.'
2 9 'Springer, J.P.'
3 1 'McKeever, B.M.'
3 2 'Navia, M.A.'
3 3 'Fitzgerald, P.M.D.'
3 4 'Springer, J.P.'
3 5 'Leu, C.-T.'
3 6 'Heimbach, J.C.'
3 7 'Herber, W.K.'
3 8 'Sigal, I.S.'
3 9 'Darke, P.L.'
4 1 'Darke, P.L.'
4 2 'Leu, C.-T.'
4 3 'Davis, L.J.'
4 4 'Heimbach, J.C.'
4 5 'Diehl, R.E.'
4 6 'Hill, W.S.'
4 7 'Dixon, R.A.F.'
4 8 'Sigal, I.S.'
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
Mandatory: yes
This data item is a pointer to _citation.id in the CITATION category.
Alias: _citation_author_citation_id (cif_core.dic, 2.0.1)
Category: citation_author
Mandatory: yes
Name of an author of the citation; relevant for journal articles, books and book chapters. The family name(s), followed by a comma and including any dynastic components, precedes the first name(s) or initial(s).
Alias: _citation_author_name (cif_core.dic, 2.0.1)
Type: line
Examples:
| Example | Detail |
|---|---|
Bleary, Percival R. |
|
O'Neil, F.K. |
|
Van den Bossche, G. |
|
Yang, D.-L. |
|
Simonov, Yu.A. |
Category: citation_author
Mandatory: no
This data item defines the order of the author's name in the list of authors of a citation.
Alias: _citation_author_ordinal (cif_core.dic, 2.0.1)
Type: int
Data items in the CITATION_EDITOR category record details about the editors associated with the books or book chapters cited in the CITATION list.
Mandatory: no
Keys: _citation_editor.citation_id _citation_editor.name
Groups: inclusive_group citation_group
Examples:
| Example | Detail |
|---|---|
loop_
_citation_editor.citation_id
_citation_editor.name
5 'McKeever, B.M.'
5 'Navia, M.A.'
5 'Fitzgerald, P.M.D.'
5 'Springer, J.P.'
|
Example 1 - hypothetical example. |
Mandatory: yes
This data item is a pointer to _citation.id in the CITATION category.
Alias: _citation_editor_citation_id (cif_core.dic, 2.0.1)
Category: citation_editor
Mandatory: no
Names of an editor of the citation; relevant for books and book chapters. The family name(s), followed by a comma and including any dynastic components, precedes the first name(s) or initial(s).
Alias: _citation_editor_name (cif_core.dic, 2.0.1)
Type: line
Examples:
| Example | Detail |
|---|---|
Bleary, Percival R. |
|
O'Neil, F.K. |
|
Van den Bossche, G. |
|
Yang, D.-L. |
|
Simonov, Yu.A. |
Category: citation_editor
Mandatory: no
This data item defines the order of the editor's name in the list of editors of a citation.
Alias: _citation_editor_ordinal (cif_core.dic, 2.0.1)
Type: int
Data items in the COMPUTING category record details about the computer programs used in the crystal structure analysis. Data items in this category would not, in general, be used in a macromolecular CIF. The category SOFTWARE, which allows a more detailed description of computer programs and their attributes to be given, would be used instead.
Mandatory: no
Keys: _computing.entry_id
Groups: inclusive_group computing_group
Examples:
| Example | Detail |
|---|---|
_computing.data_collection 'CAD-4 (Enraf-Nonius, 1989)'
_computing.cell_refinement 'CAD-4 (Enraf-Nonius, 1989)'
_computing.data_reduction 'CFEO (Solans, 1978)'
_computing.structure_solution 'SHELXS86 (Sheldrick, 1990)'
_computing.structure_refinement 'SHELXL93 (Sheldrick, 1993)'
_computing.molecular_graphics 'ORTEPII (Johnson, 1976)'
_computing.publication_material 'PARST (Nardelli, 1983)'
|
Example 1 - Rodr\'iguez-Romera, Ruiz-P\'erez & Solans [Acta Cryst. (1996), C52, 1415-1417]. |
Mandatory: yes
This data item is a pointer to _entry.id in the ENTRY category.
Category: computing
Mandatory: no
Software used for cell refinement. Give the program or package name and a brief reference.
Alias: _computing_cell_refinement (cif_core.dic, 2.0.1)
Type: text
Example:
CAD4 (Enraf-Nonius, 1989)
Category: computing
Mandatory: no
Software used for data collection. Give the program or package name and a brief reference.
Alias: _computing_data_collection (cif_core.dic, 2.0.1)
Type: text
Example:
CAD4 (Enraf-Nonius, 1989)
Category: computing
Mandatory: no
Software used for data reduction. Give the program or package name and a brief reference.
Alias: _computing_data_reduction (cif_core.dic, 2.0.1)
Type: text
Example:
DIFDAT, SORTRF, ADDREF (Hall & Stewart, 1990)
Category: computing
Mandatory: no
Software used for molecular graphics. Give the program or package name and a brief reference.
Alias: _computing_molecular_graphics (cif_core.dic, 2.0.1)
Type: text
Example:
FRODO (Jones, 1986), ORTEP (Johnson, 1965)
Category: computing
Mandatory: no
Software used for generating material for publication. Give the program or package name and a brief reference.
Alias: _computing_publication_material (cif_core.dic, 2.0.1)
Type: text
Category: computing
Mandatory: no
Software used for refinement of the structure. Give the program or package name and a brief reference.
Alias: _computing_structure_refinement (cif_core.dic, 2.0.1)
Type: text
Examples:
| Example | Detail |
|---|---|
SHELX85 (Sheldrick, 1985) |
|
X-PLOR (Brunger, 1992) |
Category: computing
Mandatory: no
Software used for solution of the structure. Give the program or package name and a brief reference.
Alias: _computing_structure_solution (cif_core.dic, 2.0.1)
Type: text
Example:
SHELX85 (Sheldrick, 1985)
Data items in the DATABASE category have been superseded by data items in the DATABASE_2 category. They are included here only for compliance with older CIFs.
Mandatory: no
Keys: _database.entry_id
Groups: inclusive_group compliance_group
Mandatory: yes
This data item is a pointer to _entry.id in the ENTRY category.
Category: database
Mandatory: no
The ASTM CODEN designator for a journal as given in the Chemical Source List maintained by the Chemical Abstracts Service.
Alias: _database_journal_ASTM (cif_core.dic, 2.0.1)
Type: line
Category: database
Mandatory: no
The journal code used in the Cambridge Structural Database.
Alias: _database_journal_CSD (cif_core.dic, 2.0.1)
Type: line
Data items in the DATABASE_2 category record details about the database identifiers of the data block. These data items are assigned by database managers and should only appear in a data block if they originate from that source. The name of this category, DATABASE_2, arose because the category name DATABASE was already in use in the core CIF dictionary, but was used differently from the way it needed to be used in the mmCIF dictionary. Since CIF data names cannot be changed once they have been adopted, a new category had to be created.
Mandatory: no
Keys: _database_2.database_id _database_2.database_code
Groups: inclusive_group database_group
Examples:
| Example | Detail |
|---|---|
_database_2.database_id 'PDB'
_database_2.database_code '5HVP'
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
Category: database_2
Mandatory: yes
An abbreviation that identifies the database.
Type: ucode
Related items: _database.code_CAS (replaces) _database.code_CSD (replaces) _database.code_ICSD (replaces) _database.code_MDF (replaces) _database.code_NBS (replaces) _database.code_PDF (replaces)
Enumeration values:
| Value | Detail |
|---|---|
CAS |
Chemical Abstracts |
CSD |
Cambridge Structural Database (organic and metal-organic compounds) |
ICSD |
Inorganic Crystal Structure Database |
MDF |
Metals Data File (metal structures) |
NDB |
Nucleic Acid Database |
NBS |
NBS (NIST) Crystal Data Database (lattice parameters) |
PDB |
Protein Data Bank |
| Powder Diffraction File (JCPDS/ICDD) | |
RCSB |
Research Collaboratory for Structural Bioinformatics |
EBI |
European Bioinformatics Institute |
Category: database_2
Mandatory: yes
The code assigned by the database identified in _database_2.database_id.
Type: line
Related items: _database.code_CAS (replaces) _database.code_CSD (replaces) _database.code_ICSD (replaces) _database.code_MDF (replaces) _database.code_NBS (replaces) _database.code_PDF (replaces)
Examples:
| Example | Detail |
|---|---|
1ABC |
|
ABCDEF |
Data items in the DATABASE_PDB_CAVEAT category record details about features of the data block flagged as 'caveats' by the Protein Data Bank (PDB). These data items are included only for consistency with PDB format files. They should appear in a data block only if that data block was created by reformatting a PDB format file.
Mandatory: no
Keys: _database_PDB_caveat.id
Groups: inclusive_group database_group pdb_group
Examples:
| Example | Detail |
|---|---|
loop_
_database_PDB_caveat.id
_database_PDB_caveat.text
1
; THE CRYSTAL TRANSFORMATION IS IN ERROR BUT IS
;
2
; UNCORRECTABLE AT THIS TIME
;
|
Example 1 - hypothetical example. |
Category: database_PDB_caveat
Mandatory: yes
A unique identifier for the PDB caveat record.
Type: int
Category: database_PDB_caveat
Mandatory: no
The full text of the PDB caveat record.
Type: text
The DATABASE_PDB_MATRIX category provides placeholders for transformation matrices and vectors used by the Protein Data Bank (PDB). These data items are included only for consistency with older PDB format files. They should appear in a data block only if that data block was created by reformatting a PDB format file.
Mandatory: no
Keys: _database_PDB_matrix.entry_id
Groups: inclusive_group database_group pdb_group
Mandatory: yes
This data item is a pointer to _entry.id in the ENTRY category.
Category: database_PDB_matrix
Mandatory: no
Sub-category: matrix
The [1][1] element of the PDB ORIGX matrix.
Type: float
Default value: 1.0
Category: database_PDB_matrix
Mandatory: no
Sub-category: matrix
The [1][2] element of the PDB ORIGX matrix.
Type: float
Default value: 0.0
Category: database_PDB_matrix
Mandatory: no
Sub-category: matrix
The [1][3] element of the PDB ORIGX matrix.
Type: float
Default value: 0.0
Category: database_PDB_matrix
Mandatory: no
Sub-category: matrix
The [2][1] element of the PDB ORIGX matrix.
Type: float
Default value: 0.0
Category: database_PDB_matrix
Mandatory: no
Sub-category: matrix
The [2][2] element of the PDB ORIGX matrix.
Type: float
Default value: 1.0
Category: database_PDB_matrix
Mandatory: no
Sub-category: matrix
The [2][3] element of the PDB ORIGX matrix.
Type: float
Default value: 0.0
Category: database_PDB_matrix
Mandatory: no
Sub-category: matrix
The [3][1] element of the PDB ORIGX matrix.
Type: float
Default value: 0.0
Category: database_PDB_matrix
Mandatory: no
Sub-category: matrix
The [3][2] element of the PDB ORIGX matrix.
Type: float
Default value: 0.0
Category: database_PDB_matrix
Mandatory: no
Sub-category: matrix
The [3][3] element of the PDB ORIGX matrix.
Type: float
Default value: 1.0
Category: database_PDB_matrix
Mandatory: no
Sub-category: vector
The [1] element of the PDB ORIGX vector.
Type: float
Default value: 0.0
Category: database_PDB_matrix
Mandatory: no
Sub-category: vector
The [2] element of the PDB ORIGX vector.
Type: float
Default value: 0.0
Category: database_PDB_matrix
Mandatory: no
Sub-category: vector
The [3] element of the PDB ORIGX vector.
Type: float
Default value: 0.0
Category: database_PDB_matrix
Mandatory: no
Sub-category: matrix
The [1][1] element of the PDB SCALE matrix.
Type: float
Default value: 1.0
Category: database_PDB_matrix
Mandatory: no
Sub-category: matrix
The [1][2] element of the PDB SCALE matrix.
Type: float
Default value: 0.0
Category: database_PDB_matrix
Mandatory: no
Sub-category: matrix
The [1][3] element of the PDB SCALE matrix.
Type: float
Default value: 0.0
Category: database_PDB_matrix
Mandatory: no
Sub-category: matrix
The [2][1] element of the PDB SCALE matrix.
Type: float
Default value: 0.0
Category: database_PDB_matrix
Mandatory: no
Sub-category: matrix
The [2][2] element of the PDB SCALE matrix.
Type: float
Default value: 1.0
Category: database_PDB_matrix
Mandatory: no
Sub-category: matrix
The [2][3] element of the PDB SCALE matrix.
Type: float
Default value: 0.0
Category: database_PDB_matrix
Mandatory: no
Sub-category: matrix
The [3][1] element of the PDB SCALE matrix.
Type: float
Default value: 0.0
Category: database_PDB_matrix
Mandatory: no
Sub-category: matrix
The [3][2] element of the PDB SCALE matrix.
Type: float
Default value: 0.0
Category: database_PDB_matrix
Mandatory: no
Sub-category: matrix
The [3][3] element of the PDB SCALE matrix.
Type: float
Default value: 1.0
Category: database_PDB_matrix
Mandatory: no
Sub-category: vector
The [1] element of the PDB SCALE vector.
Type: float
Default value: 0.0
Category: database_PDB_matrix
Mandatory: no
Sub-category: vector
The [2] element of the PDB SCALE vector.
Type: float
Default value: 0.0
Category: database_PDB_matrix
Mandatory: no
Sub-category: vector
The [3] element of the PDB SCALE vector.
Type: float
Default value: 0.0
Data items in the DATABASE_PDB_REMARK category record details about the data block as archived by the Protein Data Bank (PDB). Some data appearing in PDB REMARK records can be algorithmically extracted into the appropriate data items in the data block. These data items are included only for consistency with older PDB format files. They should appear in a data block only if that data block was created by reformatting a PDB format file.
Mandatory: no
Keys: _database_PDB_remark.id
Groups: inclusive_group database_group pdb_group
Examples:
| Example | Detail |
|---|---|
loop_
_database_PDB_remark.id
_database_PDB_remark.text
3
; REFINEMENT. BY THE RESTRAINED LEAST-SQUARES PROCEDURE OF J.
KONNERT AND W. HENDRICKSON (PROGRAM *PROLSQ*). THE R
VALUE IS 0.176 FOR 12901 REFLECTIONS IN THE RESOLUTION
RANGE 8.0 TO 2.0 ANGSTROMS WITH I .GT. SIGMA(I).
RMS DEVIATIONS FROM IDEAL VALUES (THE VALUES OF
SIGMA, IN PARENTHESES, ARE THE INPUT ESTIMATED
STANDARD DEVIATIONS THAT DETERMINE THE RELATIVE
WEIGHTS OF THE CORRESPONDING RESTRAINTS)
DISTANCE RESTRAINTS (ANGSTROMS)
BOND DISTANCE 0.018(0.020)
ANGLE DISTANCE 0.038(0.030)
PLANAR 1-4 DISTANCE 0.043(0.040)
PLANE RESTRAINT (ANGSTROMS) 0.015(0.020)
CHIRAL-CENTER RESTRAINT (ANGSTROMS**3) 0.177(0.150)
NON-BONDED CONTACT RESTRAINTS (ANGSTROMS)
SINGLE TORSION CONTACT 0.216(0.500)
MULTIPLE TORSION CONTACT 0.207(0.500)
POSSIBLE HYDROGEN BOND 0.245(0.500)
CONFORMATIONAL TORSION ANGLE RESTRAINT (DEGREES)
PLANAR (OMEGA) 2.6(3.0)
STAGGERED 17.4(15.0)
ORTHONORMAL 18.1(20.0)
;
4
; THE TWO CHAINS OF THE DIMERIC ENZYME HAS BEEN ASSIGNED THE
THE CHAIN INDICATORS *A* AND *B*.
;
# - - - - data truncated for brevity - - - -
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
Category: database_PDB_remark
Mandatory: yes
A unique identifier for the PDB remark record.
Type: int
Category: database_PDB_remark
Mandatory: no
The full text of the PDB remark record.
Type: text
Data items in the DATABASE_PDB_REV category record details about the history of the data block as archived by the Protein Data Bank (PDB). These data items are assigned by the PDB database managers and should only appear in a data block if they originate from that source.
Mandatory: no
Keys: _database_PDB_rev.num
Groups: inclusive_group database_group pdb_group
Examples:
| Example | Detail |
|---|---|
loop_
_database_PDB_rev.num
_database_PDB_rev.author_name
_database_PDB_rev.date
_database_PDB_rev.date_original
_database_PDB_rev.status
_database_PDB_rev.mod_type
1 'Fitzgerald, Paula M.D' 1991-10-15 1990-04-30
'full release' 0
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
Category: database_PDB_rev
Mandatory: no
The name of the person responsible for submitting this revision to the PDB. The family name(s) followed by a comma precedes the first name(s) or initial(s).
Type: line
Examples:
| Example | Detail |
|---|---|
Bleary, Percival R. |
|
O'Neil, F.K. |
|
Van den Bossche, G. |
|
Yang, D.-L. |
|
Simonov, Yu.A. |
Category: database_PDB_rev
Mandatory: no
Date the PDB revision took place. Taken from the REVDAT record.
Type: yyyy-mm-dd
Category: database_PDB_rev
Mandatory: no
Date the entry first entered the PDB database in the form yyyy-mm-dd. Taken from the PDB HEADER record.
Type: yyyy-mm-dd
Example:
1980-08-21
Category: database_PDB_rev
Mandatory: no
Taken from the REVDAT record. Refer to the Protein Data Bank format description at http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html for details.
Type: int
Enumeration values:
| Value | Detail |
|---|---|
0 |
initial entry |
1 |
all other types of modification |
2 |
modifications to CONECT records |
3 |
modifications affecting the coordinates or their transforms (CRYST1, ORIGX, SCALE, MTRIX, TVECT, ATOM, HETATM, SIGATM records) |
4 |
layer 1 to layer 2 revision which may affect all record types |
5 |
data uniformity processing |
| Name | Category | Mandatory |
|---|---|---|
| _database_PDB_rev.num | database_PDB_rev | yes |
| _database_PDB_rev_record.rev_num | database_PDB_rev_record | yes |
The value of _database_PDB_rev.num must uniquely and sequentially identify a record in the DATABASE_PDB_REV list. Note that this item must be a number and that modification numbers are assigned in increasing numerical order.
Type: int
Child / Parent relations:
| Child | Parent |
|---|---|
| _database_PDB_rev_record.rev_num | _database_PDB_rev.num |
Category: database_PDB_rev
Mandatory: no
The PDB code for a subsequent PDB entry that replaced the PDB file corresponding to this data block.
Type: line
Category: database_PDB_rev
Mandatory: no
The PDB code for a previous PDB entry that was replaced by the PDB file corresponding to this data block.
Type: line
Category: database_PDB_rev
Mandatory: no
The status of this revision.
Type: uline
Enumeration values:
| Value | Detail |
|---|---|
in preparation |
|
prerelease |
|
full release |
|
obsolete |
Data items in the DATABASE_PDB_REV_RECORD category record details about specific record types that were changed in a given revision of a PDB entry. These data items are assigned by the PDB database managers and should only appear in a data block if they originate from that source.
Mandatory: no
Keys: _database_PDB_rev_record.rev_num _database_PDB_rev_record.type
Groups: inclusive_group database_group pdb_group
Examples:
| Example | Detail |
|---|---|
loop_
_database_PDB_rev_record.rev_num
_database_PDB_rev_record.type
_database_PDB_rev_record.details
1 CONECT
; Error fix - incorrect connection between
atoms 2312 and 2317
;
2 MATRIX 'For consistency with 1995-08-04 style-guide'
3 ORIGX 'Based on new data from author'
|
Example 1 - hypothetical example. |
Category: database_PDB_rev_record
Mandatory: no
A description of special aspects of the revision of records in this PDB entry.
Type: text
Examples:
| Example | Detail |
|---|---|
Based on new data from author |
|
For consistency with 1995-08-04 style-guide |
|
For consistency with structural class |
Mandatory: yes
This data item is a pointer to _database_PDB_rev.num in the DATABASE_PDB_REV category.
Category: database_PDB_rev_record
Mandatory: yes
The types of records that were changed in this revision to a PDB entry.
Type: line
Examples:
| Example | Detail |
|---|---|
CRYST1 |
|
SCALE |
|
MTRIX |
|
ATOM |
|
HETATM |
The DATABASE_PDB_TVECT category provides placeholders for the TVECT matrices and vectors used by the Protein Data Bank (PDB). These data items are included only for consistency with older PDB format files. They should appear in a data block only if the data block was created by reformatting a PDB format file.
Mandatory: no
Keys: _database_PDB_tvect.id
Groups: inclusive_group database_group pdb_group
Category: database_PDB_tvect
Mandatory: no
A description of special aspects of this TVECT.
Type: text
Category: database_PDB_tvect
Mandatory: yes
The value of _database_PDB_tvect.id must uniquely identify a record in the DATABASE_PDB_TVECT list. Note that this item need not be a number; it can be any unique identifier.
Type: code
Category: database_PDB_tvect
Mandatory: no
Sub-category: vector
The [1] element of the PDB TVECT vector.
Type: float
Default value: 0.0
Category: database_PDB_tvect
Mandatory: no
Sub-category: vector
The [2] element of the PDB TVECT vector.
Type: float
Default value: 0.0
Category: database_PDB_tvect
Mandatory: no
Sub-category: vector
The [3] element of the PDB TVECT vector.
Type: float
Default value: 0.0
Data items in the DIFFRN category record details about the diffraction data and their measurement.
Mandatory: no
Keys: _diffrn.id
Groups: inclusive_group diffrn_group
Examples:
| Example | Detail |
|---|---|
_diffrn.id 'Set1'
_diffrn.ambient_temp 293(3)
_diffrn.ambient_environment
; Mother liquor from the reservoir of the vapor diffusion
experiment, mounted in room air
;
_diffrn.crystal_support
; 0.7 mm glass capillary, sealed with dental wax
;
_diffrn.crystal_treatment
; Equilibrated in rotating anode radiation enclosure for
18 hours prior to beginning of data collection
;
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
_diffrn.id 'd1'
_diffrn.details
; \q scan width (1.0 + 0.14tan\q)\%, \q scan rate 1.2\% per
min. Background counts for 5 sec on each side every scan.
;
_diffrn.ambient_temp 293
|
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. |
Category: diffrn
Mandatory: no
The gas or liquid surrounding the sample, if not air.
Alias: _diffrn_ambient_environment (cif_core.dic, 2.0.1)
Type: line
Category: diffrn
Mandatory: no
The mean temperature in kelvins at which the intensities were measured.
Alias: _diffrn_ambient_temperature (cif_core.dic, 2.0.1)
Type: float
Type conditions: esd
Units: kelvins
Related item: _diffrn.ambient_temp_esd (associated_esd)
Range: [0.0, .] [0.0, 0.0]
Category: diffrn
Mandatory: no
A description of special aspects of temperature control during data collection.
Type: text
Category: diffrn
Mandatory: no
The standard uncertainty (estimated standard deviation) of _diffrn.ambient_temp.
Type: float
Units: kelvins
Related item: _diffrn.ambient_temp (associated_value)
Mandatory: yes
This data item is a pointer to _exptl_crystal.id in the EXPTL_CRYSTAL category.
Alias: _diffrn_refln_crystal_id (cif_core.dic, 2.0.1)
Category: diffrn
Mandatory: no
The physical device used to support the crystal during data collection.
Type: text
Examples:
| Example | Detail |
|---|---|
glass capillary |
|
quartz capillary |
|
fiber |
|
metal loop |
Category: diffrn
Mandatory: no
Remarks about how the crystal was treated prior to intensity measurement. Particularly relevant when intensities were measured at low temperature.
Alias: _diffrn_crystal_treatment (cif_core.dic, 2.0.1)
Type: text
Examples:
| Example | Detail |
|---|---|
equilibrated in hutch for 24 hours |
|
flash frozen in liquid nitrogen |
|
slow cooled with direct air stream |
Category: diffrn
Mandatory: no
Special details of the diffraction measurement process. Should include information about source instability, crystal motion, degradation and so on.
Alias: _diffrn_special_details (cif_core.dic, 2.0.1)
Type: text
| Name | Category | Mandatory |
|---|---|---|
| _diffrn.id | diffrn | yes |
| _diffrn_detector.diffrn_id | diffrn_detector | yes |
| _diffrn_measurement.diffrn_id | diffrn_measurement | yes |
| _diffrn_orient_matrix.diffrn_id | diffrn_orient_matrix | yes |
| _diffrn_orient_refln.diffrn_id | diffrn_orient_refln | yes |
| _diffrn_radiation.diffrn_id | diffrn_radiation | yes |
| _diffrn_refln.diffrn_id | diffrn_refln | yes |
| _diffrn_reflns.diffrn_id | diffrn_reflns | yes |
| _diffrn_source.diffrn_id | diffrn_source | yes |
| _diffrn_standard_refln.diffrn_id | diffrn_standard_refln | yes |
| _diffrn_standards.diffrn_id | diffrn_standards | yes |
This data item uniquely identifies a set of diffraction data.
Type: code
Child / Parent relations:
Data items in the DIFFRN_ATTENUATOR category record details about the diffraction attenuator scales employed.
Mandatory: no
Keys: _diffrn_attenuator.code
Groups: inclusive_group diffrn_group
Examples:
| Example | Detail |
|---|---|
_diffrn_attenuator.code 1
_diffrn_attenuator.scale 16.976
|
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. |
| Name | Category | Mandatory |
|---|---|---|
| _diffrn_attenuator.code | diffrn_attenuator | yes |
A code associated with a particular attenuator setting. This code is referenced by the _diffrn_refln.attenuator_code which is stored with the diffraction data. See _diffrn_attenuator.scale.
Alias: _diffrn_attenuator_code (cif_core.dic, 2.0.1)
Type: code
Child / Parent relations:
| Child | Parent |
|---|---|
| _diffrn_refln.attenuator_code | _diffrn_attenuator.code |
Category: diffrn_attenuator
Mandatory: no
The scale factor applied when an intensity measurement is reduced by an attenuator identified by _diffrn_attenuator.code. The measured intensity must be multiplied by this scale to convert it to the same scale as unattenuated intensities.
Alias: _diffrn_attenuator_scale (cif_core.dic, 2.0.1)
Type: float
Range: [1.0, .] [1.0, 1.0]
Data items in the DIFFRN_DETECTOR category describe the detector used to measure the scattered radiation, including any analyser and post-sample collimation.
Mandatory: no
Keys: _diffrn_detector.diffrn_id
Groups: inclusive_group diffrn_group
Examples:
| Example | Detail |
|---|---|
_diffrn_detector.diffrn_id 'd1'
_diffrn_detector.detector 'multiwire'
_diffrn_detector.type 'Siemens'
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
Category: diffrn_detector
Mandatory: no
A description of special aspects of the radiation detector.
Alias: _diffrn_detector_details (cif_core.dic, 2.0.1)
Type: text
Category: diffrn_detector
Mandatory: no
The general class of the radiation detector.
Related items: _diffrn_radiation_detector (cifdic.c91, 1.0) _diffrn_detector (cif_core.dic, 2.0)
Type: text
Examples:
| Example | Detail |
|---|---|
photographic film |
|
scintillation counter |
|
CCD plate |
|
BF~3~ counter |
Mandatory: yes
This data item is a pointer to _diffrn.id in the DIFFRN category.
Category: diffrn_detector
Mandatory: no
The make, model or name of the detector device used.
Alias: _diffrn_detector_type (cif_core.dic, 2.0.1)
Type: text
Data items in the DIFFRN_MEASUREMENT category record details about the device used to orient and/or position the crystal during data measurement and the manner in which the diffraction data were measured.
Mandatory: no
Keys: _diffrn_measurement.diffrn_id
Groups: inclusive_group diffrn_group
Examples:
| Example | Detail |
|---|---|
_diffrn_measurement.diffrn_id 'd1'
_diffrn_measurement.device '3-circle camera'
_diffrn_measurement.device_type 'Supper model x'
_diffrn_measurement.device_details 'none'
_diffrn_measurement.method 'omega scan'
_diffrn_measurement.details
; 440 frames, 0.20 degrees, 150 sec, detector distance 12 cm,
detector angle 22.5 degrees
;
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
_diffrn_measurement.diffrn_id 's1'
_diffrn_measurement.device_type
'Philips PW1100/20 diffractometer'
_diffrn_measurement.method \q/2\q
|
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. |
Mandatory: yes
This data item is a pointer to _diffrn.id in the DIFFRN category.
Category: diffrn_measurement
Mandatory: no
A description of special aspects of the intensity measurement.
Alias: _diffrn_measurement_details (cif_core.dic, 2.0.1)
Type: text
Example:
440 frames, 0.20 degrees, 150 sec, detector
distance 12 cm, detector angle 22.5 degrees
Category: diffrn_measurement
Mandatory: no
The general class of goniometer or device used to support and orient the specimen.
Alias: _diffrn_measurement_device (cif_core.dic, 2.0.1)
Type: text
Examples:
| Example | Detail |
|---|---|
3-circle camera |
|
4-circle camera |
|
kappa-geometry camera |
|
oscillation camera |
|
precession camera |
Category: diffrn_measurement
Mandatory: no
A description of special aspects of the device used to measure the diffraction intensities.
Alias: _diffrn_measurement_device_details (cif_core.dic, 2.0.1)
Type: text
Example:
commercial goniometer modified locally to
allow for 90\% \t arc
Category: diffrn_measurement
Mandatory: no
The make, model or name of the measurement device (goniometer) used.
Alias: _diffrn_measurement_device_type (cif_core.dic, 2.0.1)
Type: text
Examples:
| Example | Detail |
|---|---|
Supper model q |
|
Huber model r |
|
Enraf-Nonius model s |
|
homemade |
Category: diffrn_measurement
Mandatory: no
Method used to measure intensities.
Alias: _diffrn_measurement_method (cif_core.dic, 2.0.1)
Type: text
Example:
profile data from theta/2theta scans
Category: diffrn_measurement
Mandatory: no
The physical device used to support the crystal during data collection.
Alias: _diffrn_measurement_specimen_support (cif_core.dic, 2.0.1)
Type: text
Examples:
| Example | Detail |
|---|---|
glass capillary |
|
quartz capillary |
|
fiber |
|
metal loop |
Data items in the DIFFRN_ORIENT_MATRIX category record details about the orientation matrix used in the measurement of the diffraction data.
Mandatory: no
Keys: _diffrn_orient_matrix.diffrn_id
Groups: inclusive_group diffrn_group
Examples:
| Example | Detail |
|---|---|
_diffrn_orient_matrix.diffrn_id set1
_diffrn_orient_matrix.type
; reciprocal axis matrix, multiplies hkl vector to generate
diffractometer xyz vector and diffractometer angles
;
_diffrn_orient_matrix.UB[1][1] -0.071479
_diffrn_orient_matrix.UB[1][2] 0.020208
_diffrn_orient_matrix.UB[1][3] 0.039076
_diffrn_orient_matrix.UB[2][1] 0.035372
_diffrn_orient_matrix.UB[2][2] 0.056209
_diffrn_orient_matrix.UB[2][3] 0.078324
_diffrn_orient_matrix.UB[3][1] -0.007470
_diffrn_orient_matrix.UB[3][2] 0.067854
_diffrn_orient_matrix.UB[3][3] -0.017832
|
Example 1 - based on CAD-4 diffractometer data obtained for Yb(S-C5H4N)2(THF)4. |
Mandatory: yes
This data item is a pointer to _diffrn.id in the DIFFRN category.
Category: diffrn_orient_matrix
Mandatory: no
A description of the orientation matrix type and how it should be applied to define the orientation of the crystal precisely with respect to the diffractometer axes.
Alias: _diffrn_orient_matrix_type (cif_core.dic, 2.0.1)
Type: text
Category: diffrn_orient_matrix
Mandatory: no
The [1][1] element of the 3x3 matrix that defines the dimensions of the reciprocal cell and its orientation with respect to the local diffractometer axes. See also _diffrn_orient_matrix.type.
Alias: _diffrn_orient_matrix_UB_11 (cif_core.dic, 2.0.1)
Type: float
Category: diffrn_orient_matrix
Mandatory: no
Sub-category: matrix
The [1][2] element of the 3x3 matrix that defines the dimensions of the reciprocal cell and its orientation with respect to the local diffractometer axes. See also _diffrn_orient_matrix.type.
Alias: _diffrn_orient_matrix_UB_12 (cif_core.dic, 2.0.1)
Type: float
Category: diffrn_orient_matrix
Mandatory: no
Sub-category: matrix
The [1][3] element of the 3x3 matrix that defines the dimensions of the reciprocal cell and its orientation with respect to the local diffractometer axes. See also _diffrn_orient_matrix.type.
Alias: _diffrn_orient_matrix_UB_13 (cif_core.dic, 2.0.1)
Type: float
Category: diffrn_orient_matrix
Mandatory: no
Sub-category: matrix
The [2][1] element of the 3x3 matrix that defines the dimensions of the reciprocal cell and its orientation with respect to the local diffractometer axes. See also _diffrn_orient_matrix.type.
Alias: _diffrn_orient_matrix_UB_21 (cif_core.dic, 2.0.1)
Type: float
Category: diffrn_orient_matrix
Mandatory: no
Sub-category: matrix
The [2][2] element of the 3x3 matrix that defines the dimensions of the reciprocal cell and its orientation with respect to the local diffractometer axes. See also _diffrn_orient_matrix.type.
Alias: _diffrn_orient_matrix_UB_22 (cif_core.dic, 2.0.1)
Type: float
Category: diffrn_orient_matrix
Mandatory: no
Sub-category: matrix
The [2][3] element of the 3x3 matrix that defines the dimensions of the reciprocal cell and its orientation with respect to the local diffractometer axes. See also _diffrn_orient_matrix.type.
Alias: _diffrn_orient_matrix_UB_23 (cif_core.dic, 2.0.1)
Type: float
Category: diffrn_orient_matrix
Mandatory: no
Sub-category: matrix
The [3][1] element of the 3x3 matrix that defines the dimensions of the reciprocal cell and its orientation with respect to the local diffractometer axes. See also _diffrn_orient_matrix.type.
Alias: _diffrn_orient_matrix_UB_31 (cif_core.dic, 2.0.1)
Type: float
Category: diffrn_orient_matrix
Mandatory: no
Sub-category: matrix
The [3][2] element of the 3x3 matrix that defines the dimensions of the reciprocal cell and its orientation with respect to the local diffractometer axes. See also _diffrn_orient_matrix.type.
Alias: _diffrn_orient_matrix_UB_32 (cif_core.dic, 2.0.1)
Type: float
Category: diffrn_orient_matrix
Mandatory: no
Sub-category: matrix
The [3][3] element of the 3x3 matrix that defines the dimensions of the reciprocal cell and its orientation with respect to the local diffractometer axes. See also _diffrn_orient_matrix.type.
Alias: _diffrn_orient_matrix_UB_33 (cif_core.dic, 2.0.1)
Type: float
Data items in the DIFFRN_ORIENT_REFLN category record details about the reflections that define the orientation matrix used in the measurement of the diffraction intensities.
Mandatory: no
Keys: _diffrn_orient_refln.diffrn_id _diffrn_orient_refln.index_h _diffrn_orient_refln.index_k _diffrn_orient_refln.index_l
Groups: inclusive_group diffrn_group
Examples:
| Example | Detail |
|---|---|
_diffrn_orient_refln.diffrn_id myset1
_diffrn_orient_refln.index_h 2
_diffrn_orient_refln.index_k 0
_diffrn_orient_refln.index_l 2
_diffrn_orient_refln.angle_chi -28.45
_diffrn_orient_refln.angle_kappa -11.32
_diffrn_orient_refln.angle_omega 5.33
_diffrn_orient_refln.angle_phi 101.78
_diffrn_orient_refln.angle_psi 0.00
_diffrn_orient_refln.angle_theta 10.66
# ... data abbreviated ...
|
Example 1 - based on CAD-4 diffractometer data obtained for Yb(S-C5H4N)2(THF)4. |
Category: diffrn_orient_refln
Mandatory: no
Diffractometer angle chi of a reflection used to define the orientation matrix in degrees. See _diffrn_orient_matrix.UB[][] and the Miller indices in the DIFFRN_ORIENT_REFLN category.
Alias: _diffrn_orient_refln_angle_chi (cif_core.dic, 2.0.1)
Type: float
Units: degrees
Dependent items: _diffrn_orient_refln.angle_kappa _diffrn_orient_refln.angle_omega _diffrn_orient_refln.angle_phi _diffrn_orient_refln.angle_psi _diffrn_orient_refln.angle_theta
Category: diffrn_orient_refln
Mandatory: no
Diffractometer angle kappa of a reflection used to define the orientation matrix in degrees. See _diffrn_orient_matrix.UB[][] and the Miller indices in the DIFFRN_ORIENT_REFLN category.
Alias: _diffrn_orient_refln_angle_kappa (cif_core.dic, 2.0.1)
Type: float
Units: degrees
Dependent items: _diffrn_orient_refln.angle_chi _diffrn_orient_refln.angle_omega _diffrn_orient_refln.angle_phi _diffrn_orient_refln.angle_psi _diffrn_orient_refln.angle_theta
Category: diffrn_orient_refln
Mandatory: no
Diffractometer angle omega of a reflection used to define the orientation matrix in degrees. See _diffrn_orient_matrix.UB[][] and the Miller indices in the DIFFRN_ORIENT_REFLN category.
Alias: _diffrn_orient_refln_angle_omega (cif_core.dic, 2.0.1)
Type: float
Units: degrees
Dependent items: _diffrn_orient_refln.angle_chi _diffrn_orient_refln.angle_kappa _diffrn_orient_refln.angle_phi _diffrn_orient_refln.angle_psi _diffrn_orient_refln.angle_theta
Category: diffrn_orient_refln
Mandatory: no
Diffractometer angle phi of a reflection used to define the orientation matrix in degrees. See _diffrn_orient_matrix.UB[][] and the Miller indices in the DIFFRN_ORIENT_REFLN category.
Alias: _diffrn_orient_refln_angle_phi (cif_core.dic, 2.0.1)
Type: float
Units: degrees
Dependent items: _diffrn_orient_refln.angle_chi _diffrn_orient_refln.angle_kappa _diffrn_orient_refln.angle_omega _diffrn_orient_refln.angle_psi _diffrn_orient_refln.angle_theta
Category: diffrn_orient_refln
Mandatory: no
Diffractometer angle psi of a reflection used to define the orientation matrix in degrees. See _diffrn_orient_matrix.UB[][] and the Miller indices in the DIFFRN_ORIENT_REFLN category.
Alias: _diffrn_orient_refln_angle_psi (cif_core.dic, 2.0.1)
Type: float
Units: degrees
Dependent items: _diffrn_orient_refln.angle_chi _diffrn_orient_refln.angle_kappa _diffrn_orient_refln.angle_omega _diffrn_orient_refln.angle_phi _diffrn_orient_refln.angle_theta
Category: diffrn_orient_refln
Mandatory: no
Diffractometer angle theta of a reflection used to define the orientation matrix in degrees. See _diffrn_orient_matrix.UB[][] and the Miller indices in the DIFFRN_ORIENT_REFLN category.
Alias: _diffrn_orient_refln_angle_theta (cif_core.dic, 2.0.1)
Type: float
Units: degrees
Dependent items: _diffrn_orient_refln.angle_chi _diffrn_orient_refln.angle_kappa _diffrn_orient_refln.angle_omega _diffrn_orient_refln.angle_phi _diffrn_orient_refln.angle_psi
Mandatory: yes
This data item is a pointer to _diffrn.id in the DIFFRN category.
Category: diffrn_orient_refln
Mandatory: yes
Sub-category: miller_index
Miller index h of a reflection used to define the orientation matrix.
Alias: _diffrn_orient_refln_index_h (cif_core.dic, 2.0.1)
Type: int
Dependent items: _diffrn_orient_refln.index_k _diffrn_orient_refln.index_l
Category: diffrn_orient_refln
Mandatory: yes
Sub-category: miller_index
Miller index k of a reflection used to define the orientation matrix.
Alias: _diffrn_orient_refln_index_k (cif_core.dic, 2.0.1)
Type: int
Dependent items: _diffrn_orient_refln.index_h _diffrn_orient_refln.index_l
Category: diffrn_orient_refln
Mandatory: yes
Sub-category: miller_index
Miller index l of a reflection used to define the orientation matrix.
Alias: _diffrn_orient_refln_index_l (cif_core.dic, 2.0.1)
Type: int
Dependent items: _diffrn_orient_refln.index_h _diffrn_orient_refln.index_l
Data items in the DIFFRN_RADIATION category describe the radiation used in measuring the diffraction intensities, its collimation and monochromatization before the sample. Post-sample treatment of the beam is described by data items in the DIFFRN_DETECTOR category.
Mandatory: no
Keys: _diffrn_radiation.diffrn_id
Groups: inclusive_group diffrn_group
Examples:
| Example | Detail |
|---|---|
_diffrn_radiation.diffrn_id 'set1'
_diffrn_radiation.collimation '0.3 mm double pinhole'
_diffrn_radiation.monochromator 'graphite'
_diffrn_radiation.type 'Cu K\a'
_diffrn_radiation.wavelength_id 1
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
_diffrn_radiation.wavelength_id 1
_diffrn_radiation.type 'Cu K\a'
_diffrn_radiation.monochromator 'graphite'
|
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. |
Category: diffrn_radiation
Mandatory: no
The collimation or focusing applied to the radiation.
Alias: _diffrn_radiation_collimation (cif_core.dic, 2.0.1)
Type: text
Examples:
| Example | Detail |
|---|---|
0.3 mm double-pinhole |
|
0.5 mm |
|
focusing mirrors |
Mandatory: yes
This data item is a pointer to _diffrn.id in the DIFFRN category.
Category: diffrn_radiation
Mandatory: no
Absorption edge in angstroms of the radiation filter used.
Alias: _diffrn_radiation_filter_edge (cif_core.dic, 2.0.1)
Type: float
Units: angstroms
Range: [0.0, .] [0.0, 0.0]
Category: diffrn_radiation
Mandatory: no
Half-width in millimetres of the incident beam in the direction perpendicular to the diffraction plane.
Alias: _diffrn_radiation_inhomogeneity (cif_core.dic, 2.0.1)
Type: float
Units: millimetres
Range: [0.0, .] [0.0, 0.0]
Category: diffrn_radiation
Mandatory: no
The method used to obtain monochromatic radiation. If a mono- chromator crystal is used, the material and the indices of the Bragg reflection are specified.
Alias: _diffrn_radiation_monochromator (cif_core.dic, 2.0.1)
Type: text
Examples:
| Example | Detail |
|---|---|
Zr filter |
|
Ge 220 |
|
none |
|
equatorial mounted graphite |
Category: diffrn_radiation
Mandatory: no
The angle in degrees, as viewed from the specimen, between the perpendicular component of the polarization and the diffraction plane. See _diffrn_radiation.polarisn_ratio.
Alias: _diffrn_radiation_polarisn_norm (cif_core.dic, 2.0.1)
Type: float
Units: degrees
Range: [0.0, .] [0.0, 0.0]
Category: diffrn_radiation
Mandatory: no
Polarization ratio of the diffraction beam incident on the crystal. This is the ratio of the perpendicularly polarized to the parallel-polarized component of the radiation. The perpendicular component forms an angle of _diffrn_radiation.polarisn_norm to the normal to the diffraction plane of the sample (i.e. the plane containing the incident and reflected beams).
Alias: _diffrn_radiation_polarisn_ratio (cif_core.dic, 2.0.1)
Type: float
Range: [0.0, .] [0.0, 0.0]
Category: diffrn_radiation
Mandatory: no
The nature of the radiation used (i.e. the name of the subatomic particle or the region of the electromagnetic spectrum). It is strongly recommended that this information is given, so that the probe radiation can be simply determined.
Alias: _diffrn_radiation_probe (cif_core.dic, 2.0.1)
Type: line
Enumeration values:
| Value | Detail |
|---|---|
x-ray |
|
neutron |
|
electron |
|
gamma |
Category: diffrn_radiation
Mandatory: no
The nature of the radiation. This is typically a description of the X-ray wavelength in Siegbahn notation.
Alias: _diffrn_radiation_type (cif_core.dic, 2.0.1)
Type: line
Examples:
| Example | Detail |
|---|---|
CuK\a |
|
Cu K\a~1~ |
|
Cu K-L~2,3~ |
|
white-beam |
Category: diffrn_radiation
Mandatory: no
The IUPAC symbol for the X-ray wavelength for the probe radiation.
Alias: _diffrn_radiation_xray_symbol (cif_core.dic, 2.0.1)
Type: line
Enumeration values:
| Value | Detail |
|---|---|
K-L~3~ |
K\a~1~ in older Siegbahn notation |
K-L~2~ |
K\a~2~ in older Siegbahn notation |
K-M~3~ |
K\b~1~ in older Siegbahn notation |
K-L~2,3~ |
use where K-L~3~ and K-L~2~ are not resolved |
Mandatory: yes
This data item is a pointer to _diffrn_radiation_wavelength.id in the DIFFRN_RADIATION_WAVELENGTH category.
Data items in the DIFFRN_RADIATION_WAVELENGTH category describe the wavelength of the radiation used to measure the diffraction intensities. Items may be looped to identify and assign weights to distinct components of a polychromatic beam.
Mandatory: no
Keys: _diffrn_radiation_wavelength.id
Groups: inclusive_group diffrn_group
Examples:
| Example | Detail |
|---|---|
_diffrn_radiation_wavelength.id 1
_diffrn_radiation_wavelength.wavelength 1.54
_diffrn_radiation_wavelength.wt 1.0
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
| Name | Category | Mandatory |
|---|---|---|
| _diffrn_radiation_wavelength.id | diffrn_radiation_wavelength | yes |
| _diffrn_radiation.wavelength_id | diffrn_radiation | yes |
| _diffrn_refln.wavelength_id | diffrn_refln | yes |
| _refln.wavelength_id | refln | yes |
The code identifying each value of _diffrn_radiation_wavelength.wavelength. Items in the DIFFRN_RADIATION_WAVELENGTH category are looped when multiple wavelengths are used. This code is used to link with the DIFFRN_REFLN category. The _diffrn_refln.wavelength_id codes must match one of the codes defined in this category.
Alias: _diffrn_radiation_wavelength_id (cif_core.dic, 2.0.1)
Type: code
Child / Parent relations:
| Child | Parent |
|---|---|
| _diffrn_radiation.wavelength_id | _diffrn_radiation_wavelength.id |
| _diffrn_refln.wavelength_id | _diffrn_radiation_wavelength.id |
| _refln.wavelength_id | _diffrn_radiation_wavelength.id |
Examples:
| Example | Detail |
|---|---|
x1 |
|
x2 |
|
neut |
Category: diffrn_radiation_wavelength
Mandatory: yes
The radiation wavelength in angstroms.
Alias: _diffrn_radiation_wavelength (cif_core.dic, 2.0.1)
Type: float
Units: angstroms
Range: [0.0, .] [0.0, 0.0]
Category: diffrn_radiation_wavelength
Mandatory: no
The relative weight of a wavelength identified by the code _diffrn_radiation_wavelength.id in the list of wavelengths.
Alias: _diffrn_radiation_wavelength_wt (cif_core.dic, 2.0.1)
Type: float
Default value: 1.0
Range: [1.0, 1.0] [0.0, 1.0] [0.0, 0.0]
Data items in the DIFFRN_REFLN category record details about the intensities in the diffraction data set identified by _diffrn_refln.diffrn_id. The DIFFRN_REFLN data items refer to individual intensity measurements and must be included in looped lists. The DIFFRN_REFLNS data items specify the parameters that apply to all intensity measurements in the particular diffraction data set identified by _diffrn_reflns.diffrn_id.
Mandatory: no
Keys: _diffrn_refln.diffrn_id _diffrn_refln.id
Groups: inclusive_group diffrn_group
Examples:
| Example | Detail |
|---|---|
_diffrn_refln.diffrn_id set1
_diffrn_refln.id 1102
_diffrn_refln.wavelength_id Cu1fixed
_diffrn_refln.angle_chi 32.21
_diffrn_refln.angle_kappa 20.12
_diffrn_refln.angle_omega 11.54
_diffrn_refln.angle_phi 176.02
_diffrn_refln.angle_psi 0.00
_diffrn_refln.angle_theta 23.08
_diffrn_refln.attenuator_code 'Ni.005'
_diffrn_refln.counts_bg_1 22
_diffrn_refln.counts_bg_2 25
_diffrn_refln.counts_net 3450
_diffrn_refln.counts_peak 321
_diffrn_refln.counts_total 3499
_diffrn_refln.detect_slit_horiz 0.04
_diffrn_refln.detect_slit_vert 0.02
_diffrn_refln.elapsed_time 1.00
_diffrn_refln.index_h 4
_diffrn_refln.index_k 0
_diffrn_refln.index_l 2
_diffrn_refln.intensity_net 202.56
_diffrn_refln.intensity_sigma 2.18
_diffrn_refln.scale_group_code A24
_diffrn_refln.scan_mode om
_diffrn_refln.scan_mode_backgd mo
_diffrn_refln.scan_rate 1.2
_diffrn_refln.scan_time_backgd 900.00
_diffrn_refln.scan_width 1.0
_diffrn_refln.sint_over_lambda 0.25426
_diffrn_refln.standard_code 1
_diffrn_refln.wavelength 1.54184
|
Example 1 - based on CAD-4 diffractometer data obtained for Yb(S-C5H4N)2(THF)4 for data set 'set1' reflection 1102. |
Category: diffrn_refln
Mandatory: no
The diffractometer angle chi of a reflection in degrees. This angle corresponds to the specified orientation matrix and the original measured cell before any subsequent cell transformations.
Alias: _diffrn_refln_angle_chi (cif_core.dic, 2.0.1)
Type: float
Units: degrees
Category: diffrn_refln
Mandatory: no
The diffractometer angle kappa of a reflection in degrees. This angle corresponds to the specified orientation matrix and the original measured cell before any subsequent cell transformations.
Alias: _diffrn_refln_angle_kappa (cif_core.dic, 2.0.1)
Type: float
Units: degrees
Category: diffrn_refln
Mandatory: no
The diffractometer angle omega of a reflection in degrees. This angle corresponds to the specified orientation matrix and the original measured cell before any subsequent cell transformations.
Alias: _diffrn_refln_angle_omega (cif_core.dic, 2.0.1)
Type: float
Units: degrees
Category: diffrn_refln
Mandatory: no
The diffractometer angle phi of a reflection in degrees. This angle corresponds to the specified orientation matrix and the original measured cell before any subsequent cell transformations.
Alias: _diffrn_refln_angle_phi (cif_core.dic, 2.0.1)
Type: float
Units: degrees
Category: diffrn_refln
Mandatory: no
The diffractometer angle psi of a reflection in degrees. This angle corresponds to the specified orientation matrix and the original measured cell before any subsequent cell transformations.
Alias: _diffrn_refln_angle_psi (cif_core.dic, 2.0.1)
Type: float
Units: degrees
Category: diffrn_refln
Mandatory: no
The diffractometer angle theta of a reflection in degrees. This angle corresponds to the specified orientation matrix and the original measured cell before any subsequent cell transformations.
Alias: _diffrn_refln_angle_theta (cif_core.dic, 2.0.1)
Type: float
Units: degrees
Mandatory: no
The code identifying the attenuator setting for this reflection. This code must match one of the _diffrn_attenuator.code values.
Alias: _diffrn_refln_attenuator_code (cif_core.dic, 2.0.1)
Category: diffrn_refln
Mandatory: no
The diffractometer counts for the measurement of the background before the peak.
Alias: _diffrn_refln_counts_bg_1 (cif_core.dic, 2.0.1)
Type: int
Range: [0, .] [0, 0]
Category: diffrn_refln
Mandatory: no
The diffractometer counts for the measurement of the background after the peak.
Alias: _diffrn_refln_counts_bg_2 (cif_core.dic, 2.0.1)
Type: int
Range: [0, .] [0, 0]
Category: diffrn_refln
Mandatory: no
The diffractometer counts for the measurement of net counts after background removal.
Alias: _diffrn_refln_counts_net (cif_core.dic, 2.0.1)
Type: int
Range: [0, .] [0, 0]
Category: diffrn_refln
Mandatory: no
The diffractometer counts for the measurement of counts for the peak scan or position.
Alias: _diffrn_refln_counts_peak (cif_core.dic, 2.0.1)
Type: int
Range: [0, .] [0, 0]
Category: diffrn_refln
Mandatory: no
The diffractometer counts for the measurement of total counts (background plus peak).
Alias: _diffrn_refln_counts_total (cif_core.dic, 2.0.1)
Type: int
Range: [0, .] [0, 0]
Category: diffrn_refln
Mandatory: no
Total slit aperture in degrees in the diffraction plane.
Alias: _diffrn_refln_detect_slit_horiz (cif_core.dic, 2.0.1)
Type: float
Units: degrees
Range: [90.0, 90.0] [0.0, 90.0] [0.0, 0.0]
Category: diffrn_refln
Mandatory: no
Total slit aperture in degrees perpendicular to the diffraction plane.
Alias: _diffrn_refln_detect_slit_vert (cif_core.dic, 2.0.1)
Type: float
Units: degrees
Range: [90.0, 90.0] [0.0, 90.0] [0.0, 0.0]
Mandatory: yes
This data item is a pointer to _diffrn.id in the DIFFRN category.
Category: diffrn_refln
Mandatory: no
Elapsed time in minutes from the start of the diffraction experiment to the measurement of this intensity.
Alias: _diffrn_refln_elapsed_time (cif_core.dic, 2.0.1)
Type: float
Units: minutes
Range: [0.0, .] [0.0, 0.0]
Category: diffrn_refln
Mandatory: yes
The value of _diffrn_refln.id must uniquely identify the reflection in the data set identified by the item _diffrn_refln.diffrn_id. Note that this item need not be a number; it can be any unique identifier.
Type: code
Category: diffrn_refln
Mandatory: yes
Sub-category: miller_index
Miller index h of a reflection. The values of the Miller indices in the DIFFRN_REFLN category need not match the values of the Miller indices in the REFLN category if a transformation of the original measured cell has taken place. Details of the cell transformation are given in _diffrn_reflns.reduction_process. See also _diffrn_reflns.transf_matrix[][].
Alias: _diffrn_refln_index_h (cif_core.dic, 2.0.1)
Type: int
Dependent items: _diffrn_refln.index_h _diffrn_refln.index_k
Category: diffrn_refln
Mandatory: yes
Sub-category: miller_index
Miller index k of a reflection. The values of the Miller indices in the DIFFRN_REFLN category need not match the values of the Miller indices in the REFLN category if a transformation of the original measured cell has taken place. Details of the cell transformation are given in _diffrn_reflns.reduction_process. See also _diffrn_reflns.transf_matrix[][].
Alias: _diffrn_refln_index_k (cif_core.dic, 2.0.1)
Type: int
Dependent items: _diffrn_refln.index_h _diffrn_refln.index_l
Category: diffrn_refln
Mandatory: yes
Sub-category: miller_index
Miller index l of a reflection. The values of the Miller indices in the DIFFRN_REFLN category need not match the values of the Miller indices in the REFLN category if a transformation of the original measured cell has taken place. Details of the cell transformation are given in _diffrn_reflns.reduction_process. See also _diffrn_reflns.transf_matrix[][].
Alias: _diffrn_refln_index_l (cif_core.dic, 2.0.1)
Type: int
Dependent items: _diffrn_refln.index_h _diffrn_refln.index_k
Category: diffrn_refln
Mandatory: no
Net intensity calculated from the diffraction counts after the attenuator and standard scales have been applied.
Alias: _diffrn_refln_intensity_net (cif_core.dic, 2.0.1)
Type: float
Range: [0, .] [0, 0]
Category: diffrn_refln
Mandatory: no
Standard uncertainty (estimated standard deviation) of the intensity calculated from the diffraction counts after the attenuator and standard scales have been applied.
Alias: _diffrn_refln_intensity_sigma (cif_core.dic, 2.0.1)
Type: float
Range: [0, .] [0, 0]
Mandatory: yes
The code identifying the scale applying to this reflection. This data item is a pointer to _diffrn_scale_group.code in the DIFFRN_SCALE_GROUP category.
Alias: _diffrn_refln_scale_group_code (cif_core.dic, 2.0.1)
Category: diffrn_refln
Mandatory: no
The code identifying the mode of scanning for measurements using a diffractometer. See _diffrn_refln.scan_width and _diffrn_refln.scan_mode_backgd.
Alias: _diffrn_refln_scan_mode (cif_core.dic, 2.0.1)
Type: ucode
Enumeration values:
| Value | Detail |
|---|---|
om |
omega scan |
ot |
omega/2theta scan |
q |
Q scans (arbitrary reciprocal directions) |
Category: diffrn_refln
Mandatory: no
The code identifying the mode of scanning a reflection to measure the background intensity.
Alias: _diffrn_refln_scan_mode_backgd (cif_core.dic, 2.0.1)
Type: ucode
Enumeration values:
| Value | Detail |
|---|---|
st |
stationary counter background |
mo |
moving counter background |
Category: diffrn_refln
Mandatory: no
The rate of scanning a reflection in degrees per minute to measure the intensity.
Alias: _diffrn_refln_scan_rate (cif_core.dic, 2.0.1)
Type: float
Units: degrees_per_minute
Category: diffrn_refln
Mandatory: no
The time spent measuring each background in seconds.
Alias: _diffrn_refln_scan_time_backgd (cif_core.dic, 2.0.1)
Type: float
Units: seconds
Category: diffrn_refln
Mandatory: no
The scan width in degrees of the scan mode defined by the code _diffrn_refln.scan_mode.
Alias: _diffrn_refln_scan_width (cif_core.dic, 2.0.1)
Type: float
Units: degrees
Range: [90.0, 90.0] [0.0, 90.0] [0.0, 0.0]
Category: diffrn_refln
Mandatory: no
The (sin theta)/lambda value in reciprocal angstroms for this reflection.
Alias: _diffrn_refln_sint/lambda (cif_core.dic, 2.0.1)
Type: float
Units: reciprocal_angstroms
Range: [0.0, .] [0.0, 0.0]
Mandatory: yes
The code identifying that this reflection was measured as a standard intensity. This data item is a pointer to _diffrn_standard_refln.code in the DIFFRN_STANDARD_REFLN category.
Alias: _diffrn_refln_standard_code (cif_core.dic, 2.0.1)
Category: diffrn_refln
Mandatory: no
The mean wavelength in angstroms of the radiation used to measure the intensity of this reflection. This is an important parameter for data collected using energy-dispersive detectors or the Laue method.
Alias: _diffrn_refln_wavelength (cif_core.dic, 2.0.1)
Type: float
Units: angstroms
Range: [0.0, .] [0.0, 0.0]
Mandatory: yes
This data item is a pointer to _diffrn_radiation.wavelength_id in the DIFFRN_RADIATION category.
Alias: _diffrn_refln_wavelength_id (cif_core.dic, 2.0.1)
Data items in the DIFFRN_REFLNS category record details about the set of intensities measured in the diffraction experiment. The DIFFRN_REFLN data items refer to individual intensity measurements and must be included in looped lists. The DIFFRN_REFLNS data items specify the parameters that apply to all intensity measurements in a diffraction data set.
Mandatory: no
Keys: _diffrn_reflns.diffrn_id
Groups: inclusive_group diffrn_group
Category: diffrn_reflns
Mandatory: no
The residual [sum|avdel(I)| / sum|av(I)|] for symmetry-equivalent reflections used to calculate the average intensity av(I). The avdel(I) term is the average absolute difference between av(I) and the individual symmetry-equivalent intensities.
Alias: _diffrn_reflns_av_R_equivalents (cif_core.dic, 2.0.1)
Type: float
Range: [0.0, .] [0.0, 0.0]
Category: diffrn_reflns
Mandatory: no
Measure [sum|sigma(I)|/sum|net(I)|] for all measured reflections.
Alias: _diffrn_reflns_av_sigmaI/netI (cif_core.dic, 2.0.1)
Type: float
Range: [0.0, .] [0.0, 0.0]
Mandatory: yes
This data item is a pointer to _diffrn.id in the DIFFRN category.
Category: diffrn_reflns
Mandatory: no
The maximum value of the Miller index h for the reflection data specified by _diffrn_refln.index_h.
Alias: _diffrn_reflns_limit_h_max (cif_core.dic, 2.0.1)
Type: int
Category: diffrn_reflns
Mandatory: no
The minimum value of the Miller index h for the reflection data specified by _diffrn_refln.index_h.
Alias: _diffrn_reflns_limit_h_min (cif_core.dic, 2.0.1)
Type: int
Category: diffrn_reflns
Mandatory: no
The maximum value of the Miller index k for the reflection data specified by _diffrn_refln.index_k.
Alias: _diffrn_reflns_limit_k_max (cif_core.dic, 2.0.1)
Type: int
Category: diffrn_reflns
Mandatory: no
The minimum value of the Miller index k for the reflection data specified by _diffrn_refln.index_k.
Alias: _diffrn_reflns_limit_k_min (cif_core.dic, 2.0.1)
Type: int
Category: diffrn_reflns
Mandatory: no
The maximum value of the Miller index l for the reflection data specified by _diffrn_refln.index_l.
Alias: _diffrn_reflns_limit_l_max (cif_core.dic, 2.0.1)
Type: int
Category: diffrn_reflns
Mandatory: no
The minimum value of the Miller index l for the reflection data specified by _diffrn_refln.index_l.
Alias: _diffrn_reflns_limit_l_min (cif_core.dic, 2.0.1)
Type: int
Category: diffrn_reflns
Mandatory: no
The total number of measured intensities, excluding reflections that are classified as systematically absent.
Alias: _diffrn_reflns_number (cif_core.dic, 2.0.1)
Type: int
Range: [0, .] [0, 0]
Category: diffrn_reflns
Mandatory: no
A description of the process used to reduce the intensity data into structure-factor magnitudes.
Alias: _diffrn_reflns_reduction_process (cif_core.dic, 2.0.1)
Type: text
Example:
data averaged using Fisher test
Category: diffrn_reflns
Mandatory: no
Maximum theta angle in degrees for the measured diffraction intensities.
Alias: _diffrn_reflns_theta_max (cif_core.dic, 2.0.1)
Type: float
Units: degrees
Range: [90.0, 90.0] [0.0, 90.0] [0.0, 0.0]
Category: diffrn_reflns
Mandatory: no
Minimum theta angle in degrees for the measured diffraction intensities.
Alias: _diffrn_reflns_theta_min (cif_core.dic, 2.0.1)
Type: float
Units: degrees
Range: [90.0, 90.0] [0.0, 90.0] [0.0, 0.0]
Category: diffrn_reflns
Mandatory: no
Sub-category: matrix
The [1][1] element of the 3x3 matrix used to transform Miller indices in the DIFFRN_REFLN category into the Miller indices in the REFLN category.
Alias: _diffrn_reflns_transf_matrix_11 (cif_core.dic, 2.0.1)
Type: float
Category: diffrn_reflns
Mandatory: no
Sub-category: matrix
The [1][2] element of the 3x3 matrix used to transform Miller indices in the DIFFRN_REFLN category into the Miller indices in the REFLN category.
Alias: _diffrn_reflns_transf_matrix_12 (cif_core.dic, 2.0.1)
Type: float
Category: diffrn_reflns
Mandatory: no
Sub-category: matrix
The [1][3] element of the 3x3 matrix used to transform Miller indices in the DIFFRN_REFLN category into the Miller indices in the REFLN category.
Alias: _diffrn_reflns_transf_matrix_13 (cif_core.dic, 2.0.1)
Type: float
Category: diffrn_reflns
Mandatory: no
Sub-category: matrix
The [2][1] element of the 3x3 matrix used to transform Miller indices in the DIFFRN_REFLN category into the Miller indices in the REFLN category.
Alias: _diffrn_reflns_transf_matrix_21 (cif_core.dic, 2.0.1)
Type: float
Category: diffrn_reflns
Mandatory: no
Sub-category: matrix
The [2][2] element of the 3x3 matrix used to transform Miller indices in the DIFFRN_REFLN category into the Miller indices in the REFLN category.
Alias: _diffrn_reflns_transf_matrix_22 (cif_core.dic, 2.0.1)
Type: float
Category: diffrn_reflns
Mandatory: no
Sub-category: matrix
The [2][3] element of the 3x3 matrix used to transform Miller indices in the DIFFRN_REFLN category into the Miller indices in the REFLN category.
Alias: _diffrn_reflns_transf_matrix_23 (cif_core.dic, 2.0.1)
Type: float
Category: diffrn_reflns
Mandatory: no
Sub-category: matrix
The [3][1] element of the 3x3 matrix used to transform Miller indices in the DIFFRN_REFLN category into the Miller indices in the REFLN category.
Alias: _diffrn_reflns_transf_matrix_31 (cif_core.dic, 2.0.1)
Type: float
Category: diffrn_reflns
Mandatory: no
Sub-category: matrix
The [3][2] element of the 3x3 matrix used to transform Miller indices in the DIFFRN_REFLN category into the Miller indices in the REFLN category.
Alias: _diffrn_reflns_transf_matrix_32 (cif_core.dic, 2.0.1)
Type: float
Category: diffrn_reflns
Mandatory: no
Sub-category: matrix
The [3][3] element of the 3x3 matrix used to transform Miller indices in the DIFFRN_REFLN category into the Miller indices in the REFLN category.
Alias: _diffrn_reflns_transf_matrix_33 (cif_core.dic, 2.0.1)
Type: float
Data items in the DIFFRN_SCALE_GROUP category record details of the scaling factors applied to place all intensities in the reflection lists on a common scale. Scaling groups might, for example, correspond to each film in a multi-film data set or each crystal in a multi-crystal data set.
Mandatory: no
Keys: _diffrn_scale_group.code
Groups: inclusive_group diffrn_group
Examples:
| Example | Detail |
|---|---|
_diffrn_scale_group.code A24
_diffrn_scale_group.I_net 1.021
|
Example 1 - based on CAD-4 diffractometer data obtained for Yb(S-C5H4N)2(THF)4. |
| Name | Category | Mandatory |
|---|---|---|
| _diffrn_scale_group.code | diffrn_scale_group | yes |
| _diffrn_refln.scale_group_code | diffrn_refln | yes |
The value of _diffrn_scale_group.code must uniquely identify a record in the DIFFRN_SCALE_GROUP list. Note that this item need not be a number; it can be any unique identifier.
Alias: _diffrn_scale_group_code (cif_core.dic, 2.0.1)
Type: code
Child / Parent relations:
| Child | Parent |
|---|---|
| _diffrn_refln.scale_group_code | _diffrn_scale_group.code |
Examples:
| Example | Detail |
|---|---|
1 |
|
2 |
|
c1 |
|
c2 |
Category: diffrn_scale_group
Mandatory: no
The scale for a specific measurement group which is to be multiplied with the net intensity to place all intensities in the DIFFRN_REFLN or REFLN list on a common scale.
Alias: _diffrn_scale_group_I_net (cif_core.dic, 2.0.1)
Type: float
Range: [0.0, .] [0.0, 0.0]
Data items in the DIFFRN_SOURCE category record details of the source of radiation used in the diffraction experiment.
Mandatory: no
Keys: _diffrn_source.diffrn_id
Groups: inclusive_group diffrn_group
Examples:
| Example | Detail |
|---|---|
_diffrn_source.diffrn_id 's1'
_diffrn_source.source 'rotating anode'
_diffrn_source.type 'Rigaku RU-200'
_diffrn_source.power 50
_diffrn_source.current 180
_diffrn_source.size '8mm x 0.4 mm broad-focus'
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
Category: diffrn_source
Mandatory: no
The current in milliamperes at which the radiation source was operated.
Alias: _diffrn_source_current (cif_core.dic, 2.0.1)
Type: float
Units: milliamperes
Category: diffrn_source
Mandatory: no
A description of special aspects of the radiation source used.
Alias: _diffrn_source_details (cif_core.dic, 2.0.1)
Type: text
Mandatory: yes
This data item is a pointer to _diffrn.id in the DIFFRN category.
Category: diffrn_source
Mandatory: no
The power in kilowatts at which the radiation source was operated.
Alias: _diffrn_source_power (cif_core.dic, 2.0.1)
Type: float
Units: kilowatts
Category: diffrn_source
Mandatory: no
The dimensions of the source as viewed from the sample.
Alias: _diffrn_source_size (cif_core.dic, 2.0.1)
Type: text
Examples:
| Example | Detail |
|---|---|
8mm x 0.4 mm fine-focus |
|
broad focus |
Category: diffrn_source
Mandatory: no
The general class of the radiation source.
Related items: _diffrn_radiation_source (cifdic.c91, 1.0) _diffrn_source (cif_core.dic, 2.0)
Type: text
Examples:
| Example | Detail |
|---|---|
sealed X-ray tube |
|
nuclear reactor |
|
spallation source |
|
electron microscope |
|
rotating-anode X-ray tube |
|
synchrotron |
Category: diffrn_source
Mandatory: no
The chemical element symbol for the X-ray target (usually the anode) used to generate X-rays. This can also be used for spallation sources.
Alias: _diffrn_source_target (cif_core.dic, 2.0.1)
Type: code
Enumeration values:
| Value | Detail |
|---|---|
H |
|
He |
|
Li |
|
Be |
|
B |
|
C |
|
N |
|
O |
|
F |
|
Ne |
|
Na |
|
Mg |
|
Al |
|
Si |
|
P |
|
S |
|
Cl |
|
Ar |
|
K |
|
Ca |
|
Sc |
|
Ti |
|
V |
|
Cr |
|
Mn |
|
Fe |
|
Co |
|
Ni |
|
Cu |
|
Zn |
|
Ga |
|
Ge |
|
As |
|
Se |
|
Br |
|
Kr |
|
Rb |
|
Sr |
|
Y |
|
Zr |
|
Nb |
|
Mo |
|
Tc |
|
Ru |
|
Rh |
|
Pd |
|
Ag |
|
Cd |
|
In |
|
Sn |
|
Sb |
|
Te |
|
I |
|
Xe |
|
Cs |
|
Ba |
|
La |
|
Ce |
|
Pr |
|
Nd |
|
Pm |
|
Sm |
|
Eu |
|
Gd |
|
Tb |
|
Dy |
|
Ho |
|
Er |
|
Tm |
|
Yb |
|
Lu |
|
Hf |
|
Ta |
|
W |
|
Re |
|
Os |
|
Ir |
|
Pt |
|
Au |
|
Hg |
|
Tl |
|
Pb |
|
Bi |
|
Po |
|
At |
|
Rn |
|
Fr |
|
Ra |
|
Ac |
|
Th |
|
Pa |
|
U |
|
Np |
|
Pu |
|
Am |
|
Cm |
|
Bk |
|
Cf |
|
Es |
|
Fm |
|
Md |
|
No |
|
Lr |
Category: diffrn_source
Mandatory: no
The make, model or name of the source of radiation.
Alias: _diffrn_source_type (cif_core.dic, 2.0.1)
Type: text
Examples:
| Example | Detail |
|---|---|
NSLS beamline X8C |
|
Rigaku RU200 |
Category: diffrn_source
Mandatory: no
The voltage in kilovolts at which the radiation source was operated.
Alias: _diffrn_source_voltage (cif_core.dic, 2.0.1)
Type: float
Units: kilovolts
Data items in the DIFFRN_STANDARD_REFLN category record details about the reflections treated as standards during the measurement of a set of diffraction intensities. Note that these are the individual standard reflections, not the results of the analysis of the standard reflections.
Mandatory: no
Keys: _diffrn_standard_refln.diffrn_id _diffrn_standard_refln.code
Groups: inclusive_group diffrn_group
Examples:
| Example | Detail |
|---|---|
loop_
_diffrn_standard_refln.diffrn_id
_diffrn_standard_refln.code
_diffrn_standard_refln.index_h
_diffrn_standard_refln.index_k
_diffrn_standard_refln.index_l
s1 1 3 2 4
s1 1 1 9 1
s1 1 3 0 10
|
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. |
| Name | Category | Mandatory |
|---|---|---|
| _diffrn_standard_refln.code | diffrn_standard_refln | yes |
| _diffrn_refln.standard_code | diffrn_refln | yes |
The code identifying a reflection measured as a standard reflection with the indices _diffrn_standard_refln.index_h, _diffrn_standard_refln.index_k and _diffrn_standard_refln.index_l. This is the same code as the _diffrn_refln.standard_code in the DIFFRN_REFLN list.
Alias: _diffrn_standard_refln_code (cif_core.dic, 2.0.1)
Type: code
Child / Parent relations:
| Child | Parent |
|---|---|
| _diffrn_refln.standard_code | _diffrn_standard_refln.code |
Examples:
| Example | Detail |
|---|---|
1 |
|
2 |
|
c1 |
|
c2 |
Mandatory: yes
This data item is a pointer to _diffrn.id in the DIFFRN category.
Category: diffrn_standard_refln
Mandatory: yes
Sub-category: miller_index
Miller index h of a standard reflection used in the diffraction measurement process.
Alias: _diffrn_standard_refln_index_h (cif_core.dic, 2.0.1)
Type: int
Dependent items: _diffrn_standard_refln.index_k _diffrn_standard_refln.index_l
Category: diffrn_standard_refln
Mandatory: yes
Sub-category: miller_index
Miller index k of a standard reflection used in the diffraction measurement process.
Alias: _diffrn_standard_refln_index_k (cif_core.dic, 2.0.1)
Type: int
Dependent items: _diffrn_standard_refln.index_h _diffrn_standard_refln.index_l
Category: diffrn_standard_refln
Mandatory: yes
Sub-category: miller_index
Miller index l of a standard reflection used in the diffraction measurement process.
Alias: _diffrn_standard_refln_index_l (cif_core.dic, 2.0.1)
Type: int
Dependent items: _diffrn_standard_refln.index_h _diffrn_standard_refln.index_k
Data items in the DIFFRN_STANDARDS category record details about the set of standard reflections used to monitor intensity stability during the measurement of diffraction intensities. Note that these records describe properties common to the set of standard reflections, not the standard reflections themselves.
Mandatory: no
Keys: _diffrn_standards.diffrn_id
Groups: inclusive_group diffrn_group
Examples:
| Example | Detail |
|---|---|
_diffrn_standards.diffrn_id 's1'
_diffrn_standards.number 3
_diffrn_standards.interval_time 120
_diffrn_standards.decay_% 0
|
Example 1 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. |
Mandatory: yes
This data item is a pointer to _diffrn.id in the DIFFRN category.
Category: diffrn_standards
Mandatory: no
The percentage decrease in the mean of the intensities for the set of standard reflections from the start of the measurement process to the end. This value usually affords a measure of the overall decay in crystal quality during the diffraction measurement process. Negative values are used in exceptional instances where the final intensities are greater than the initial ones.
Alias: _diffrn_standards_decay_% (cif_core.dic, 2.0.1)
Type: float
Range: [100.0, 100.0] [., 100.0]
Category: diffrn_standards
Mandatory: no
The number of reflection intensities between the measurement of standard reflection intensities.
Alias: _diffrn_standards_interval_count (cif_core.dic, 2.0.1)
Type: int
Range: [0, .] [0, 0]
Category: diffrn_standards
Mandatory: no
The time in minutes between the measurement of standard reflection intensities.
Alias: _diffrn_standards_interval_time (cif_core.dic, 2.0.1)
Type: float
Units: minutes
Range: [0, .] [0, 0]
Category: diffrn_standards
Mandatory: no
The number of unique standard reflections used during the measurement of the diffraction intensities.
Alias: _diffrn_standards_number (cif_core.dic, 2.0.1)
Type: int
Range: [0, .] [0, 0]
Category: diffrn_standards
Mandatory: no
The standard uncertainty (estimated standard deviation) of the individual mean standard scales applied to the intensity data.
Alias: _diffrn_standards_scale_sigma (cif_core.dic, 2.0.1)
Type: float
Range: [0.0, .] [0.0, 0.0]
Data items in the ENTITY category record details (such as chemical composition, name and source) about the molecular entities that are present in the crystallographic structure. Items in the various ENTITY subcategories provide a full chemical description of these molecular entities. Entities are of three types: polymer, non-polymer and water. Note that the water category includes only water; ordered solvent such as sulfate ion or acetone would be described as individual non-polymer entities. The ENTITY category is specific to macromolecular CIF applications and replaces the function of the CHEMICAL category in the CIF core. It is important to remember that the ENTITY data are not the result of the crystallographic experiment; those results are represented by the ATOM_SITE data items. ENTITY data items describe the chemistry of the molecules under investigation and can most usefully be thought of as the ideal groups to which the structure is restrained or constrained during refinement. It is also important to remember that entities do not correspond directly to the enumeration of the contents of the asymmetric unit. Entities are described only once, even in those structures that contain multiple observations of an entity. The STRUCT_ASYM data items, which reference the entity list, describe and label the contents of the asymmetric unit.
Mandatory: no
Keys: _entity.id
Groups: inclusive_group entity_group
Examples:
| Example | Detail |
|---|---|
loop_
_entity.id
_entity.type
_entity.formula_weight
_entity.details
1 polymer 10916
; The enzymatically competent form of HIV
protease is a dimer. This entity
corresponds to one monomer of an active dimer.
;
2 non-polymer '762' .
3 water 18 .
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
Category: entity
Mandatory: no
A description of special aspects of the entity.
Type: text
Category: entity
Mandatory: no
Formula mass in daltons of the entity.
Type: float
Range: [1.0, .] [1.0, 1.0]
| Name | Category | Mandatory |
|---|---|---|
| _entity.id | entity | yes |
| _atom_site.label_entity_id | atom_site | no |
| _entity_keywords.entity_id | entity_keywords | yes |
| _entity_link.entity_id_1 | entity_link | yes |
| _entity_link.entity_id_2 | entity_link | yes |
| _entity_name_com.entity_id | entity_name_com | yes |
| _entity_name_sys.entity_id | entity_name_sys | yes |
| _entity_poly.entity_id | entity_poly | yes |
| _entity_poly_seq.entity_id | entity_poly_seq | yes |
| _entity_src_gen.entity_id | entity_src_gen | yes |
| _entity_src_nat.entity_id | entity_src_nat | yes |
| _struct_asym.entity_id | struct_asym | yes |
| _struct_ref.entity_id | struct_ref | yes |
The value of _entity.id must uniquely identify a record in the ENTITY list. Note that this item need not be a number; it can be any unique identifier.
Type: code
Child / Parent relations:
Category: entity
Mandatory: no
The method by which the sample for the entity was produced. Entities isolated directly from natural sources (tissues, soil samples etc.) are expected to have further information in the ENTITY_SRC_NAT category. Entities isolated from genetically manipulated sources are expected to have further information in the ENTITY_SRC_GEN category.
Type: ucode
Enumeration values:
| Value | Detail |
|---|---|
nat |
entity isolated from a natural source |
man |
entity isolated from a genetically manipulated source |
syn |
entity obtained synthetically |
Category: entity
Mandatory: no
Defines the type of the entity. Polymer entities are expected to have corresponding ENTITY_POLY and associated entries. Non-polymer entities are expected to have corresponding CHEM_COMP and associated entries. Water entities are not expected to have corresponding entries in the ENTITY category.
Type: ucode
Enumeration values:
| Value | Detail |
|---|---|
polymer |
entity is a polymer |
non-polymer |
entity is not a polymer |
water |
water in the solvent model |
Data items in the ENTITY_KEYWORDS category specify keywords relevant to the molecular entities. Note that this list of keywords is separate from the list that is used for the STRUCT_BIOL data items and is intended to provide only the information that one would know about the molecular entity *if one did not know its structure*. Hence polypeptides are simply polypeptides, not cytokines or beta-alpha-barrels, and polyribonucleic acids are simply poly-RNA, not transfer- RNA.
Mandatory: no
Keys: _entity_keywords.entity_id _entity_keywords.text
Groups: inclusive_group entity_group
Examples:
| Example | Detail |
|---|---|
loop_
_entity_keywords.entity_id
_entity_keywords.text
1 'polypeptide'
2 'natural product, inhibitor, reduced peptide'
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
Mandatory: yes
This data item is a pointer to _entity.id in the ENTITY category.
Category: entity_keywords
Mandatory: no
Keywords describing this entity.
Type: text
Examples:
| Example | Detail |
|---|---|
polypeptide |
|
natural product |
|
polysaccharide |
Data items in the ENTITY_LINK category give details about the links between entities.
Mandatory: no
Keys: _entity_link.link_id
Groups: inclusive_group chem_link_group
Mandatory: yes
This data item is a pointer to _chem_link.id in the CHEM_LINK category.
Category: entity_link
Mandatory: no
A description of special aspects of a link between chemical components in the structure.
Type: text
Mandatory: yes
The entity ID of the first of the two entities joined by the link. This data item is a pointer to _entity.id in the ENTITY category.
Mandatory: yes
The entity ID of the second of the two entities joined by the link. This data item is a pointer to _entity.id in the ENTITY category.
Mandatory: no
For a polymer entity, the sequence number in the first of the two entities containing the link. This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category.
Mandatory: no
For a polymer entity, the sequence number in the second of the two entities containing the link. This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category.
Data items in the ENTITY_NAME_COM category record the common name or names associated with the entity. In some cases, the entity name may not be the same as the name of the biological structure. For example, haemoglobin alpha chain would be the entity common name, not haemoglobin.
Mandatory: no
Keys: _entity_name_com.entity_id _entity_name_com.name
Groups: inclusive_group entity_group
Examples:
| Example | Detail |
|---|---|
loop_
_entity_name_com.entity_id
_entity_name_com.name
1 'HIV-1 protease monomer'
1 'HIV-1 PR monomer'
2 'acetyl-pepstatin'
2 'acetyl-Ile-Val-Asp-Statine-Ala-Ile-Statine'
3 'water'
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
Mandatory: yes
This data item is a pointer to _entity.id in the ENTITY category.
Category: entity_name_com
Mandatory: yes
A common name for the entity.
Type: text
Examples:
| Example | Detail |
|---|---|
HIV protease monomer |
|
hemoglobin alpha chain |
|
2-fluoro-1,4-dichloro benzene |
|
arbutin |
Data items in the ENTITY_NAME_SYS category record the systematic name or names associated with the entity and the system that was used to construct the systematic name. In some cases, the entity name may not be the same as the name of the biological structure.
Mandatory: no
Keys: _entity_name_sys.entity_id _entity_name_sys.name
Groups: inclusive_group entity_group
Examples:
| Example | Detail |
|---|---|
loop_
_entity_name_sys.entity_id
_entity_name_sys.name
1 'EC 3.4.23.16'
2 'acetyl-Ile-Val-Asp-Sta-Ala-Ile-Sta'
3 water
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
Mandatory: yes
This data item is a pointer to _entity.id in the ENTITY category.
Category: entity_name_sys
Mandatory: yes
The systematic name for the entity.
Type: text
Examples:
| Example | Detail |
|---|---|
hydroquinone-beta-D-pyranoside |
|
EC 2.1.1.1 |
|
2-fluoro-1,4-dichlorobenzene |
Category: entity_name_sys
Mandatory: no
The system used to generate the systematic name of the entity.
Type: text
Examples:
| Example | Detail |
|---|---|
Chemical Abstracts conventions |
|
enzyme convention |
|
Sigma catalog |
Data items in the ENTITY_POLY category record details about the polymer, such as the type of the polymer, the number of monomers and whether it has nonstandard features.
Mandatory: no
Keys: _entity_poly.entity_id
Groups: inclusive_group entity_group
Examples:
| Example | Detail |
|---|---|
loop_
_entity_poly.entity_id
_entity_poly.type
_entity_poly.nstd_chirality
_entity_poly.nstd_linkage
_entity_poly.nstd_monomer
_entity_poly.type_details
1 polypeptide(L) no no no .
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
Mandatory: yes
This data item is a pointer to _entity.id in the ENTITY category.
Category: entity_poly
Mandatory: no
A flag to indicate whether the polymer contains at least one monomer unit with chirality different from that specified in _entity_poly.type.
Type: ucode
Enumeration values:
| Value | Detail |
|---|---|
no |
polymer contains no monomers with different chirality |
n |
abbreviation for "no" |
yes |
polymer contains at least one monomer with different chirality |
y |
abbreviation for "yes" |
Category: entity_poly
Mandatory: no
A flag to indicate whether the polymer contains at least one monomer-to-monomer link different from that implied by _entity_poly.type.
Type: ucode
Enumeration values:
| Value | Detail |
|---|---|
no |
polymer contains no different links |
n |
abbreviation for "no" |
yes |
polymer contains at least one different link |
y |
abbreviation for "yes" |
Category: entity_poly
Mandatory: no
A flag to indicate whether the polymer contains at least one monomer that is not considered standard.
Type: ucode
Enumeration values:
| Value | Detail |
|---|---|
no |
polymer contains no nonstandard monomers |
n |
abbreviation for "no" |
yes |
polymer contains at least one nonstandard monomer |
y |
abbreviation for "yes" |
Category: entity_poly
Mandatory: no
The number of monomers in the polymer.
Type: int
Range: [1, .] [1, 1]
Category: entity_poly
Mandatory: no
The type of the polymer.
Type: ucode
Enumeration values:
| Value | Detail |
|---|---|
polypeptide(D) |
|
polypeptide(L) |
|
polydeoxyribonucleotide |
|
polyribonucleotide |
|
polysaccharide(D) |
|
polysaccharide(L) |
|
other |
Category: entity_poly
Mandatory: no
A description of special aspects of the polymer type.
Type: text
Examples:
| Example | Detail |
|---|---|
monomer Ala 16 is a D-amino acid |
|
the oligomer contains alternating RNA and DNA units |
Data items in the ENTITY_POLY_SEQ category specify the sequence of monomers in a polymer. Allowance is made for the possibility of microheterogeneity in a sample by allowing a given sequence number to be correlated with more than one monomer ID. The corresponding ATOM_SITE entries should reflect this heterogeneity.
Mandatory: no
Keys: _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id
Groups: inclusive_group entity_group
Examples:
| Example | Detail |
|---|---|
loop_
_entity_poly_seq.entity_id
_entity_poly_seq.num
_entity_poly_seq.mon_id
1 1 PRO 1 2 GLN 1 3 ILE 1 4 THR 1 5 LEU
1 6 TRP 1 7 GLN 1 8 ARG 1 9 PRO 1 10 LEU
1 11 VAL 1 12 THR 1 13 ILE 1 14 LYS 1 15 ILE
1 16 GLY 1 17 GLY 1 18 GLN 1 19 LEU 1 20 LYS
1 21 GLU 1 22 ALA 1 23 LEU 1 24 LEU 1 25 ASP
# - - - - data truncated for brevity - - - -
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
Mandatory: yes
This data item is a pointer to _entity.id in the ENTITY category.
Category: entity_poly_seq
Mandatory: no
A flag to indicate whether this monomer in the polymer is heterogeneous in sequence. This would be rare.
Type: ucode
Default value: no
Enumeration values:
| Value | Detail |
|---|---|
no |
sequence is not heterogeneous at this monomer |
n |
abbreviation for "no" |
yes |
sequence is heterogeneous at this monomer |
y |
abbreviation for "yes" |
Mandatory: yes
This data item is a pointer to _chem_comp.id in the CHEM_COMP category.
| Name | Category | Mandatory |
|---|---|---|
| _entity_poly_seq.num | entity_poly_seq | yes |
| _atom_site.label_seq_id | atom_site | no |
| _entity_link.entity_seq_num_1 | entity_link | no |
| _entity_link.entity_seq_num_2 | entity_link | no |
| _geom_angle.atom_site_label_seq_id_1 | geom_angle | no |
| _geom_angle.atom_site_label_seq_id_2 | geom_angle | no |
| _geom_angle.atom_site_label_seq_id_3 | geom_angle | no |
| _geom_bond.atom_site_label_seq_id_1 | geom_bond | no |
| _geom_bond.atom_site_label_seq_id_2 | geom_bond | no |
| _geom_contact.atom_site_label_seq_id_1 | geom_contact | no |
| _geom_contact.atom_site_label_seq_id_2 | geom_contact | no |
| _geom_hbond.atom_site_label_seq_id_A | geom_hbond | no |
| _geom_hbond.atom_site_label_seq_id_D | geom_hbond | no |
| _geom_hbond.atom_site_label_seq_id_H | geom_hbond | no |
| _geom_torsion.atom_site_label_seq_id_1 | geom_torsion | no |
| _geom_torsion.atom_site_label_seq_id_2 | geom_torsion | no |
| _geom_torsion.atom_site_label_seq_id_3 | geom_torsion | no |
| _geom_torsion.atom_site_label_seq_id_4 | geom_torsion | no |
| _struct_conf.beg_label_seq_id | struct_conf | yes |
| _struct_conf.end_label_seq_id | struct_conf | yes |
| _struct_conn.ptnr1_label_seq_id | struct_conn | yes |
| _struct_conn.ptnr2_label_seq_id | struct_conn | yes |
| _struct_mon_nucl.label_seq_id | struct_mon_nucl | yes |
| _struct_mon_prot.label_seq_id | struct_mon_prot | yes |
| _struct_mon_prot_cis.label_seq_id | struct_mon_prot_cis | yes |
| _struct_ncs_dom_lim.beg_label_seq_id | struct_ncs_dom_lim | yes |
| _struct_ncs_dom_lim.end_label_seq_id | struct_ncs_dom_lim | yes |
| _struct_ref_seq.seq_align_beg | struct_ref_seq | yes |
| _struct_ref_seq.seq_align_end | struct_ref_seq | yes |
| _struct_ref_seq_dif.seq_num | struct_ref_seq_dif | yes |
| _struct_sheet_hbond.range_1_beg_label_seq_id | struct_sheet_hbond | yes |
| _struct_sheet_hbond.range_1_end_label_seq_id | struct_sheet_hbond | yes |
| _struct_sheet_hbond.range_2_beg_label_seq_id | struct_sheet_hbond | yes |
| _struct_sheet_hbond.range_2_end_label_seq_id | struct_sheet_hbond | yes |
| _struct_sheet_range.beg_label_seq_id | struct_sheet_range | yes |
| _struct_sheet_range.end_label_seq_id | struct_sheet_range | yes |
| _struct_site_gen.label_seq_id | struct_site_gen | yes |
The value of _entity_poly_seq.num must uniquely and sequentially identify a record in the ENTITY_POLY_SEQ list. Note that this item must be a number and that the sequence numbers must progress in increasing numerical order.
Type: int
Child / Parent relations:
Range: [1, .] [1, 1]
Data items in the ENTITY_SRC_GEN category record details of the source from which the entity was obtained in cases where the source was genetically manipulated. The following are treated separately: items pertaining to the tissue from which the gene was obtained, items pertaining to the host organism for gene expression and items pertaining to the actual producing organism (plasmid).
Mandatory: no
Keys: _entity_src_gen.entity_id
Groups: inclusive_group entity_group
Examples:
| Example | Detail |
|---|---|
loop_
_entity_src_gen.entity_id
_entity_src_gen.gene_src_common_name
_entity_src_gen.gene_src_genus
_entity_src_gen.gene_src_species
_entity_src_gen.gene_src_strain
_entity_src_gen.host_org_common_name
_entity_src_gen.host_org_genus
_entity_src_gen.host_org_species
_entity_src_gen.plasmid_name
1 'HIV-1' '?' '?' 'NY-5'
'bacteria' 'Escherichia' 'coli' 'pB322'
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
Mandatory: yes
This data item is a pointer to _entity.id in the ENTITY category.
Category: entity_src_gen
Mandatory: no
The common name of the natural organism from which the gene was obtained.
Type: text
Examples:
| Example | Detail |
|---|---|
man |
|
yeast |
|
bacteria |
Category: entity_src_gen
Mandatory: no
A description of special aspects of the natural organism from which the gene was obtained.
Type: text
Category: entity_src_gen
Mandatory: no
The genus of the natural organism from which the gene was obtained.
Type: text
Examples:
| Example | Detail |
|---|---|
Homo |
|
Saccharomyces |
|
Escherichia |
Category: entity_src_gen
Mandatory: no
The species of the natural organism from which the gene was obtained.
Type: text
Examples:
| Example | Detail |
|---|---|
sapiens |
|
cerevisiae |
|
coli |
Category: entity_src_gen
Mandatory: no
The strain of the natural organism from which the gene was obtained, if relevant.
Type: text
Examples:
| Example | Detail |
|---|---|
DH5a |
|
BMH 71-18 |
Category: entity_src_gen
Mandatory: no
The tissue of the natural organism from which the gene was obtained.
Type: text
Examples:
| Example | Detail |
|---|---|
heart |
|
liver |
|
eye lens |
Category: entity_src_gen
Mandatory: no
The subcellular fraction of the tissue of the natural organism from which the gene was obtained.
Type: text
Examples:
| Example | Detail |
|---|---|
mitochondria |
|
nucleus |
|
membrane |
Category: entity_src_gen
Mandatory: no
The common name of the organism that served as host for the production of the entity.
Type: text
Examples:
| Example | Detail |
|---|---|
yeast |
|
bacteria |
Category: entity_src_gen
Mandatory: no
A description of special aspects of the organism that served as host for the production of the entity.
Type: text
Category: entity_src_gen
Mandatory: no
The genus of the organism that served as host for the production of the entity.
Type: text
Examples:
| Example | Detail |
|---|---|
Saccharomyces |
|
Escherichia |
Category: entity_src_gen
Mandatory: no
The species of the organism that served as host for the production of the entity.
Type: text
Examples:
| Example | Detail |
|---|---|
cerevisiae |
|
coli |
Category: entity_src_gen
Mandatory: no
The strain of the organism that served as host for the production of the entity.
Type: text
Examples:
| Example | Detail |
|---|---|
DH5a |
|
BMH 71-18 |
Category: entity_src_gen
Mandatory: no
A description of special aspects of the plasmid that produced the entity in the host organism.
Type: text
Category: entity_src_gen
Mandatory: no
The name of the plasmid that produced the entity in the host organism.
Type: text
Examples:
| Example | Detail |
|---|---|
pET3C |
|
pT123sab |
Data items in the ENTITY_SRC_NAT category record details of the source from which the entity was obtained in cases where the entity was isolated directly from a natural tissue.
Mandatory: no
Keys: _entity_src_nat.entity_id
Groups: inclusive_group entity_group
Examples:
| Example | Detail |
|---|---|
loop_
_entity_src_nat.entity_id
_entity_src_nat.common_name
_entity_src_nat.genus
_entity_src_nat.species
_entity_src_nat.details
2 'bacteria' 'Actinomycetes' '?'
; Acetyl-pepstatin was isolated by Dr. K. Oda, Osaka
Prefecture University, and provided to us by Dr. Ben
Dunn, University of Florida, and Dr. J. Kay, University
of Wales.
;
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
Category: entity_src_nat
Mandatory: yes
The common name of the organism from which the entity was isolated.
Type: text
Examples:
| Example | Detail |
|---|---|
man |
|
yeast |
|
bacteria |
Category: entity_src_nat
Mandatory: no
A description of special aspects of the organism from which the entity was isolated.
Type: text
Mandatory: yes
This data item is a pointer to _entity.id in the ENTITY category.
Category: entity_src_nat
Mandatory: yes
The genus of the organism from which the entity was isolated.
Type: text
Examples:
| Example | Detail |
|---|---|
Homo |
|
Saccharomyces |
|
Escherichia |
Category: entity_src_nat
Mandatory: yes
The species of the organism from which the entity was isolated.
Type: text
Examples:
| Example | Detail |
|---|---|
sapiens |
|
cerevisiae |
|
coli |
Category: entity_src_nat
Mandatory: yes
The strain of the organism from which the entity was isolated.
Type: text
Examples:
| Example | Detail |
|---|---|
DH5a |
|
BMH 71-18 |
Category: entity_src_nat
Mandatory: yes
The tissue of the organism from which the entity was isolated.
Type: text
Examples:
| Example | Detail |
|---|---|
heart |
|
liver |
|
eye lens |
Category: entity_src_nat
Mandatory: yes
The subcellular fraction of the tissue of the organism from which the entity was isolated.
Type: text
Examples:
| Example | Detail |
|---|---|
mitochondria |
|
nucleus |
|
membrane |
There is only one item in the ENTRY category, _entry.id. This data item gives a name to this entry and is indirectly a key to the categories (such as CELL, GEOM, EXPTL) that describe information pertinent to the entire data block.
Mandatory: no
Keys: _entry.id
Groups: inclusive_group entry_group
Examples:
| Example | Detail |
|---|---|
_entry.id '5HVP'
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
_entry.id 'TOZ'
|
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. |
| Name | Category | Mandatory |
|---|---|---|
| _entry.id | entry | yes |
| _atom_sites.entry_id | atom_sites | yes |
| _cell.entry_id | cell | yes |
| _cell_measurement.entry_id | cell_measurement | yes |
| _chemical.entry_id | chemical | yes |
| _chemical_formula.entry_id | chemical_formula | yes |
| _computing.entry_id | computing | yes |
| _database.entry_id | database | yes |
| _database_PDB_matrix.entry_id | database_PDB_matrix | yes |
| _entry_link.entry_id | entry_link | yes |
| _exptl.entry_id | exptl | yes |
| _geom.entry_id | geom | yes |
| _journal.entry_id | journal | yes |
| _phasing_averaging.entry_id | phasing_averaging | yes |
| _phasing_isomorphous.entry_id | phasing_isomorphous | yes |
| _phasing_MAD.entry_id | phasing_MAD | yes |
| _phasing_MIR.entry_id | phasing_MIR | yes |
| _publ.entry_id | publ | yes |
| _publ_manuscript_incl.entry_id | publ_manuscript_incl | yes |
| _refine.entry_id | refine | yes |
| _refine_analyze.entry_id | refine_analyze | yes |
| _reflns.entry_id | reflns | yes |
| _struct.entry_id | struct | yes |
| _struct_keywords.entry_id | struct_keywords | yes |
| _struct_mon_details.entry_id | struct_mon_details | yes |
| _symmetry.entry_id | symmetry | yes |
The value of _entry.id identifies the data block. Note that this item need not be a number; it can be any unique identifier.
Alias: _audit_block_code (cif_core.dic, 2.0.1)
Type: code
Child / Parent relations:
Data items in the ENTRY_LINK category record the relationships between the current data block identified by _entry.id and other data blocks within the current file which may be referenced in the current data block.
Mandatory: no
Keys: _entry_link.id _entry_link.entry_id
Groups: inclusive_group entry_group
Examples:
| Example | Detail |
|---|---|
loop_
_entry_link.id
_entry_link.entry_id
_entry_link.details
KSE_COM KSE_TEXT
'experimental data common to ref./mod. structures'
KSE_REF KSE_TEXT 'reference structure'
KSE_MOD KSE_TEXT 'modulated structure'
|
Example 1 - example file for the one-dimensional incommensurately modulated structure of K~2~SeO~4~. |
Mandatory: yes
This data item is a pointer to _entry.id in the ENTRY category.
Category: entry_link
Mandatory: yes
The value of _entry_link.id identifies a data block related to the current data block.
Alias: _audit_link_block_code (cif_core.dic, 2.0.1)
Type: code
Category: entry_link
Mandatory: no
A description of the relationship between the data blocks identified by _entry_link.id and _entry_link.entry_id.
Alias: _audit_link_block_description (cif_core.dic, 2.0.1)
Type: text
Data items in the EXPTL category record details about the experimental work prior to the intensity measurements and details about the absorption-correction technique employed.
Mandatory: no
Keys: _exptl.entry_id
Groups: inclusive_group exptl_group
Examples:
| Example | Detail |
|---|---|
_exptl.entry_id datablock1
_exptl.absorpt_coefficient_mu 1.22
_exptl.absorpt_correction_T_max 0.896
_exptl.absorpt_correction_T_min 0.802
_exptl.absorpt_correction_type integration
_exptl.absorpt_process_details
; Gaussian grid method from SHELX76
Sheldrick, G. M., "SHELX-76: structure determination and
refinement program", Cambridge University, UK, 1976
;
_exptl.crystals_number 1
_exptl.details
; Enraf-Nonius LT2 liquid nitrogen variable-temperature
device used
;
_exptl.method 'single-crystal x-ray diffraction'
_exptl.method_details
; graphite monochromatized Cu K(alpha) fixed tube and
Enraf-Nonius CAD4 diffractometer used
;
|
Example 1 - based on laboratory records for Yb(S-C5H4N)2(THF)4. |
Category: exptl
Mandatory: no
The absorption coefficient mu in reciprocal millimetres calculated from the atomic content of the cell, the density and the radiation wavelength.
Alias: _exptl_absorpt_coefficient_mu (cif_core.dic, 2.0.1)
Type: float
Units: reciprocal_millimetres
Range: [0.0, .] [0.0, 0.0]
Category: exptl
Mandatory: no
The maximum transmission factor for the crystal and radiation. The maximum and minimum transmission factors are also referred to as the absorption correction A or 1/A*.
Alias: _exptl_absorpt_correction_T_max (cif_core.dic, 2.0.1)
Type: float
Range: [1.0, 1.0] [0.0, 1.0] [0.0, 0.0]
Category: exptl
Mandatory: no
The minimum transmission factor for the crystal and radiation. The maximum and minimum transmission factors are also referred to as the absorption correction A or 1/A*.
Alias: _exptl_absorpt_correction_T_min (cif_core.dic, 2.0.1)
Type: float
Range: [1.0, 1.0] [0.0, 1.0] [0.0, 0.0]
Category: exptl
Mandatory: no
The absorption correction type and method. The value 'empirical' should NOT be used unless more detailed information is not available.
Alias: _exptl_absorpt_correction_type (cif_core.dic, 2.0.1)
Type: ucode
Enumeration values:
| Value | Detail |
|---|---|
analytical |
analytical from crystal shape |
cylinder |
cylindrical |
empirical |
empirical from intensities |
gaussian |
Gaussian from crystal shape |
integration |
integration from crystal shape |
multi-scan |
symmetry-related measurements |
none |
no correction applied |
numerical |
numerical from crystal shape |
psi-scan |
psi-scan corrections |
refdelf |
refined from delta-F |
sphere |
spherical |
Category: exptl
Mandatory: no
Description of the absorption process applied to the intensities. A literature reference should be supplied for psi-scan techniques.
Alias: _exptl_absorpt_process_details (cif_core.dic, 2.0.1)
Type: text
Example:
Tompa analytical
Mandatory: yes
This data item is a pointer to _entry.id in the ENTRY category.
Category: exptl
Mandatory: no
The total number of crystals used in the measurement of intensities.
Alias: _exptl_crystals_number (cif_core.dic, 2.0.1)
Type: int
Range: [1, .] [1, 1]
Category: exptl
Mandatory: no
Any special information about the experimental work prior to the intensity measurement. See also _exptl_crystal.preparation.
Alias: _exptl_special_details (cif_core.dic, 2.0.1)
Type: text
Category: exptl
Mandatory: yes
The method used in the experiment.
Type: line
Examples:
| Example | Detail |
|---|---|
single-crystal x-ray diffraction |
|
single-crystal neutron diffraction |
|
single-crystal electron diffraction |
|
fiber x-ray diffraction |
|
fiber neutron diffraction |
|
fiber electron diffraction |
|
single-crystal joint x-ray and neutron diffraction |
|
single-crystal joint x-ray and electron diffraction |
|
solution nmr |
|
solid-state nmr |
|
theoretical model |
|
other |
Category: exptl
Mandatory: no
A description of special aspects of the experimental method.
Type: text
Examples:
| Example | Detail |
|---|---|
29 structures |
|
minimized average structure |
Data items in the EXPTL_CRYSTAL category record the results of experimental measurements on the crystal or crystals used, such as shape, size or density.
Mandatory: no
Keys: _exptl_crystal.id
Groups: inclusive_group exptl_group
Examples:
| Example | Detail |
|---|---|
_exptl_crystal.id xst2l
_exptl_crystal.colour 'pale yellow'
_exptl_crystal.density_diffrn 1.113
_exptl_crystal.density_Matthews 1.01
_exptl_crystal.density_meas 1.11
_exptl_crystal.density_meas_temp 294.5
_exptl_crystal.density_method 'neutral buoyancy'
_exptl_crystal.density_percent_sol 0.15
# P = 1 - (1.23*N*MMass) / V
_exptl_crystal.description 'hexagonal rod, uncut'
_exptl_crystal.F_000 202
_exptl_crystal.preparation
; hanging drop, crystal soaked in 10% ethylene glycol for
10 h, then placed in nylon loop at data collection time
;
_exptl_crystal.size_max 0.30
_exptl_crystal.size_mid 0.20
_exptl_crystal.size_min 0.05
_exptl_crystal.size_rad 0.025
|
Example 1 - based on laboratory records for Yb(S-C5H4N)2(THF)4. |
_exptl_crystal.density_meas_gt 2.5
_exptl_crystal.density_meas_lt 5.0
|
Example 2 - using separate items to define upper and lower limits for a value. |
_exptl_crystal.density_meas_temp_lt 300 |
Example 3 - here the density was measured at some unspecified temperature below room temperature. |
Category: exptl_crystal
Mandatory: no
The colour of the crystal.
Alias: _exptl_crystal_colour (cif_core.dic, 2.0.1)
Type: line
Example:
dark green
Category: exptl_crystal
Mandatory: no
Density values calculated from the crystal cell and contents. The units are megagrams per cubic metre (grams per cubic centimetre).
Alias: _exptl_crystal_density_diffrn (cif_core.dic, 2.0.1)
Type: float
Range: [0.0, .] [0.0, 0.0]
Category: exptl_crystal
Mandatory: no
The density of the crystal, expressed as the ratio of the volume of the asymmetric unit to the molecular mass of a monomer of the structure, in units of angstroms3 per dalton. Ref: Matthews, B. W. (1968). J. Mol. Biol. 33, 491-497.
Type: float
Category: exptl_crystal
Mandatory: no
The method used to measure _exptl_crystal.density_meas.
Alias: _exptl_crystal_density_method (cif_core.dic, 2.0.1)
Type: text
Category: exptl_crystal
Mandatory: no
Density value P calculated from the crystal cell and contents, expressed as per cent solvent. P = 1 - (1.23 N MMass) / V N = the number of molecules in the unit cell MMass = the molecular mass of each molecule (gm/mole) V = the volume of the unit cell (A3) 1.23 = a conversion factor evaluated as: (0.74 cm3/g) (1024 A3/cm3) -------------------------------------- (6.02*1023) molecules/mole where 0.74 is an assumed value for the partial specific volume of the molecule
Type: float
Range: [0.0, .] [0.0, 0.0]
Category: exptl_crystal
Mandatory: no
A description of the quality and habit of the crystal. The crystal dimensions should not normally be reported here; use instead the specific items in the EXPTL_CRYSTAL category relating to size for the gross dimensions of the crystal and data items in the EXPTL_CRYSTAL_FACE category to describe the relationship between individual faces.
Alias: _exptl_crystal_description (cif_core.dic, 2.0.1)
Type: text
Category: exptl_crystal
Mandatory: no
The effective number of electrons in the crystal unit cell contributing to F(000). This may contain dispersion contributions and is calculated as F(000) = [ sum (fr2 + fi2) ]1/2 fr = real part of the scattering factors at theta = 0 degree fi = imaginary part of the scattering factors at theta = 0 degree the sum is taken over each atom in the unit cell
Alias: _exptl_crystal_F_000 (cif_core.dic, 2.0.1)
Type: int
Range: [1, .] [1, 1]
| Name | Category | Mandatory |
|---|---|---|
| _exptl_crystal.id | exptl_crystal | yes |
| _exptl_crystal_face.crystal_id | exptl_crystal_face | yes |
| _exptl_crystal_grow.crystal_id | exptl_crystal_grow | yes |
| _exptl_crystal_grow_comp.crystal_id | exptl_crystal_grow_comp | yes |
| _diffrn.crystal_id | diffrn | yes |
| _refln.crystal_id | refln | yes |
The value of _exptl_crystal.id must uniquely identify a record in the EXPTL_CRYSTAL list. Note that this item need not be a number; it can be any unique identifier.
Alias: _exptl_crystal_id (cif_core.dic, 2.0.1)
Type: code
Child / Parent relations:
Category: exptl_crystal
Mandatory: no
Details of crystal growth and preparation of the crystal (e.g. mounting) prior to the intensity measurements.
Alias: _exptl_crystal_preparation (cif_core.dic, 2.0.1)
Type: text
Example:
mounted in an argon-filled quartz capillary
Category: exptl_crystal
Mandatory: no
The maximum dimension of the crystal. This item may appear in a list with _exptl_crystal.id if multiple crystals are used in the experiment.
Alias: _exptl_crystal_size_max (cif_core.dic, 2.0.1)
Type: float
Units: millimetres
Range: [0.0, .] [0.0, 0.0]
Category: exptl_crystal
Mandatory: no
The medial dimension of the crystal. This item may appear in a list with _exptl_crystal.id if multiple crystals are used in the experiment.
Alias: _exptl_crystal_size_mid (cif_core.dic, 2.0.1)
Type: float
Units: millimetres
Range: [0.0, .] [0.0, 0.0]
Category: exptl_crystal
Mandatory: no
The minimum dimension of the crystal. This item may appear in a list with _exptl_crystal.id if multiple crystals are used in the experiment.
Alias: _exptl_crystal_size_min (cif_core.dic, 2.0.1)
Type: float
Units: millimetres
Range: [0.0, .] [0.0, 0.0]
Category: exptl_crystal
Mandatory: no
The radius of the crystal, if the crystal is a sphere or a cylinder. This item may appear in a list with _exptl_crystal.id if multiple crystals are used in the experiment.
Alias: _exptl_crystal_size_rad (cif_core.dic, 2.0.1)
Type: float
Units: millimetres
Range: [0.0, .] [0.0, 0.0]
Data items in the EXPTL_CRYSTAL_FACE category record details of the crystal faces.
Mandatory: no
Keys: _exptl_crystal_face.crystal_id _exptl_crystal_face.index_h _exptl_crystal_face.index_k _exptl_crystal_face.index_l
Groups: inclusive_group exptl_group
Examples:
| Example | Detail |
|---|---|
_exptl_crystal_face.crystal_id xstl1
_exptl_crystal_face.index_h 1
_exptl_crystal_face.index_k 0
_exptl_crystal_face.index_l 0
_exptl_crystal_face.diffr_chi 42.56
_exptl_crystal_face.diffr_kappa 30.23
_exptl_crystal_face.diffr_phi -125.56
_exptl_crystal_face.diffr_psi -0.34
_exptl_crystal_face.perp_dist 0.025
|
Example 1 - based on laboratory records for Yb(S-C5H4N)2(THF)4 for the 100 face of crystal xstl1. |
Mandatory: yes
This data item is a pointer to _exptl_crystal.id in the EXPTL_CRYSTAL category.
Category: exptl_crystal_face
Mandatory: no
The chi diffractometer setting angle in degrees for a specific crystal face associated with _exptl_crystal_face.perp_dist.
Alias: _exptl_crystal_face_diffr_chi (cif_core.dic, 2.0.1)
Type: float
Units: degrees
Category: exptl_crystal_face
Mandatory: no
The kappa diffractometer setting angle in degrees for a specific crystal face associated with _exptl_crystal_face.perp_dist.
Alias: _exptl_crystal_face_diffr_kappa (cif_core.dic, 2.0.1)
Type: float
Units: degrees
Category: exptl_crystal_face
Mandatory: no
The phi diffractometer setting angle in degrees for a specific crystal face associated with _exptl_crystal_face.perp_dist.
Alias: _exptl_crystal_face_diffr_phi (cif_core.dic, 2.0.1)
Type: float
Units: degrees
Category: exptl_crystal_face
Mandatory: no
The psi diffractometer setting angle in degrees for a specific crystal face associated with _exptl_crystal_face.perp_dist.
Alias: _exptl_crystal_face_diffr_psi (cif_core.dic, 2.0.1)
Type: float
Units: degrees
Category: exptl_crystal_face
Mandatory: yes
Sub-category: miller_index
Miller index h of the crystal face associated with the value _exptl_crystal_face.perp_dist.
Alias: _exptl_crystal_face_index_h (cif_core.dic, 2.0.1)
Type: int
Dependent items: _exptl_crystal_face.index_k _exptl_crystal_face.index_l
Category: exptl_crystal_face
Mandatory: yes
Sub-category: miller_index
Miller index k of the crystal face associated with the value _exptl_crystal_face.perp_dist.
Alias: _exptl_crystal_face_index_k (cif_core.dic, 2.0.1)
Type: int
Dependent items: _exptl_crystal_face.index_h _exptl_crystal_face.index_l
Category: exptl_crystal_face
Mandatory: yes
Sub-category: miller_index
Miller index l of the crystal face associated with the value _exptl_crystal_face.perp_dist.
Alias: _exptl_crystal_face_index_l (cif_core.dic, 2.0.1)
Type: int
Dependent items: _exptl_crystal_face.index_h _exptl_crystal_face.index_k
Category: exptl_crystal_face
Mandatory: no
The perpendicular distance in millimetres from the face to the centre of rotation of the crystal.
Alias: _exptl_crystal_face_perp_dist (cif_core.dic, 2.0.1)
Type: float
Units: millimetres
Range: [0.0, .] [0.0, 0.0]
Data items in the EXPTL_CRYSTAL_GROW category record details about the conditions and methods used to grow the crystal.
Mandatory: no
Keys: _exptl_crystal_grow.crystal_id
Groups: inclusive_group exptl_group
Examples:
| Example | Detail |
|---|---|
_exptl_crystal_grow.crystal_id 1
_exptl_crystal_grow.method 'hanging drop'
_exptl_crystal_grow.apparatus 'Linbro plates'
_exptl_crystal_grow.atmosphere 'room air'
_exptl_crystal_grow.pH 4.7
_exptl_crystal_grow.temp 18(3)
_exptl_crystal_grow.time 'approximately 2 days'
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
Category: exptl_crystal_grow
Mandatory: no
The physical apparatus in which the crystal was grown.
Type: text
Examples:
| Example | Detail |
|---|---|
Linbro plate |
|
sandwich box |
|
ACA plates |
Category: exptl_crystal_grow
Mandatory: no
The nature of the gas or gas mixture in which the crystal was grown.
Type: text
Examples:
| Example | Detail |
|---|---|
room air |
|
nitrogen |
|
argon |
Mandatory: yes
This data item is a pointer to _exptl_crystal.id in the EXPTL_CRYSTAL category.
Category: exptl_crystal_grow
Mandatory: no
A description of special aspects of the crystal growth.
Type: text
Examples:
| Example | Detail |
|---|---|
Solution 2 was prepared as a well solution and
mixed. A droplet containing 2 \ml of solution
1 was delivered onto a cover slip; 2 \ml of
solution 2 was added to the droplet without
mixing.
|
|
Crystal plates were originally stored at room
temperature for 1 week but no nucleation
occurred. They were then transferred to 4
degrees C, at which temperature well formed
single crystals grew in 2 days.
|
|
The dependence on pH for successful crystal
growth is very sharp. At pH 7.4 only showers
of tiny crystals grew, at pH 7.5 well formed
single crystals grew, at pH 7.6 no
crystallization occurred at all.
|
Category: exptl_crystal_grow
Mandatory: no
The method used to grow the crystals.
Type: text
Examples:
| Example | Detail |
|---|---|
batch precipitation |
|
batch dialysis |
|
hanging drop vapor diffusion |
|
sitting drop vapor diffusion |
Category: exptl_crystal_grow
Mandatory: no
A literature reference that describes the method used to grow the crystals.
Type: text
Examples:
| Example | Detail |
|---|---|
McPherson et al., 1988 |
Category: exptl_crystal_grow
Mandatory: no
The pH at which the crystal was grown. If more than one pH was employed during the crystallization process, the final pH should be noted here and the protocol involving multiple pH values should be described in _exptl_crystal_grow.details.
Type: float
Range: [0.0, .] [0.0, 0.0]
Examples:
| Example | Detail |
|---|---|
7.4 |
|
7.6 |
|
4.3 |
Category: exptl_crystal_grow
Mandatory: no
The ambient pressure in kilopascals at which the crystal was grown.
Type: float
Type conditions: esd
Units: kilopascals
Related item: _exptl_crystal_grow.pressure_esd (associated_esd)
Range: [0.0, .] [0.0, 0.0]
Category: exptl_crystal_grow
Mandatory: no
The standard uncertainty (estimated standard deviation) of _exptl_crystal_grow.pressure.
Type: float
Units: kilopascals
Related item: _exptl_crystal_grow.pressure (associated_value)
Category: exptl_crystal_grow
Mandatory: no
A description of the protocol used for seeding the crystal growth.
Type: text
Examples:
| Example | Detail |
|---|---|
macroseeding |
|
Microcrystals were introduced from a previous
crystal growth experiment by transfer with a
human hair.
|
Category: exptl_crystal_grow
Mandatory: no
A literature reference that describes the protocol used to seed the crystal.
Type: text
Example:
Stura et al., 1989
Category: exptl_crystal_grow
Mandatory: no
The temperature in kelvins at which the crystal was grown. If more than one temperature was employed during the crystallization process, the final temperature should be noted here and the protocol involving multiple temperatures should be described in _exptl_crystal_grow.details.
Type: float
Type conditions: esd
Units: kelvins
Related item: _exptl_crystal_grow.temp_esd (associated_esd)
Range: [0.0, .] [0.0, 0.0]
Category: exptl_crystal_grow
Mandatory: no
A description of special aspects of temperature control during crystal growth.
Type: text
Category: exptl_crystal_grow
Mandatory: no
The standard uncertainty (estimated standard deviation) of _exptl_crystal_grow.temp.
Type: float
Units: kelvins
Related item: _exptl_crystal_grow.temp (associated_value)
Category: exptl_crystal_grow
Mandatory: no
The approximate time that the crystal took to grow to the size used for data collection.
Type: text
Examples:
| Example | Detail |
|---|---|
overnight |
|
2-4 days |
|
6 months |
Data items in the EXPTL_CRYSTAL_GROW_COMP category record details about the components of the solutions that were 'mixed' (by whatever means) to produce the crystal. In general, solution 1 is the solution that contains the molecule to be crystallized and solution 2 is the solution that contains the precipitant. However, the number of solutions required to describe the crystallization protocol is not limited to 2. Details of the crystallization protocol should be given in _exptl_crystal_grow_comp.details using the solutions described in EXPTL_CRYSTAL_GROW_COMP.
Mandatory: no
Keys: _exptl_crystal_grow_comp.id _exptl_crystal_grow_comp.crystal_id
Groups: inclusive_group exptl_group
Examples:
| Example | Detail |
|---|---|
loop_
_exptl_crystal_grow_comp.crystal_id
_exptl_crystal_grow_comp.id
_exptl_crystal_grow_comp.sol_id
_exptl_crystal_grow_comp.name
_exptl_crystal_grow_comp.volume
_exptl_crystal_grow_comp.conc
_exptl_crystal_grow_comp.details
1 1 1 'HIV-1 protease' '0.002 ml' '6 mg/ml'
; The protein solution was in a buffer containing 25 mM NaCl,
100 mM NaMES/ MES buffer, pH 7.5, 3 mM NaAzide
;
1 2 2 'NaCl' '0.200 ml' '4 M' 'in 3 mM NaAzide'
1 3 2 'Acetic Acid' '0.047 ml' '100 mM' 'in 3 mM NaAzide'
1 4 2 'Na Acetate' '0.053 ml' '100 mM'
; in 3 mM NaAzide. Buffer components were mixed to produce a
pH of 4.7 according to a ratio calculated from the pKa. The
actual pH of solution 2 was not measured.
;
1 5 2 'water' '0.700 ml' 'neat' 'in 3 mM NaAzide'
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
Category: exptl_crystal_grow_comp
Mandatory: no
The concentration of the solution component.
Type: line
Examples:
| Example | Detail |
|---|---|
200 \ml |
|
0.1 ml |
Category: exptl_crystal_grow_comp
Mandatory: no
A description of any special aspects of the solution component. When the solution component is the one that contains the macromolecule, this could be the specification of the buffer in which the macromolecule was stored. When the solution component is a buffer component, this could be the methods (or formula) used to achieve a desired pH.
Type: text
Examples:
| Example | Detail |
|---|---|
in 3 mM NaAzide |
|
The protein solution was in a buffer
containing 25 mM NaCl, 100 mM NaMES/MES
buffer, pH 7.5, 3 mM NaAzide
|
|
in 3 mM NaAzide. Buffer components were mixed
to produce a pH of 4.7 according to a ratio
calculated from the pKa. The actual pH of
solution 2 was not measured.
|
Mandatory: yes
This data item is a pointer to _exptl_crystal.id in the EXPTL_CRYSTAL category.
Category: exptl_crystal_grow_comp
Mandatory: yes
The value of _exptl_crystal_grow_comp.id must uniquely identify each item in the EXPTL_CRYSTAL_GROW_COMP list. Note that this item need not be a number; it can be any unique identifier.
Type: line
Examples:
| Example | Detail |
|---|---|
1 |
|
A |
|
protein in buffer |
Category: exptl_crystal_grow_comp
Mandatory: no
A common name for the component of the solution.
Type: line
Examples:
| Example | Detail |
|---|---|
protein in buffer |
|
acetic acid |
Category: exptl_crystal_grow_comp
Mandatory: no
An identifier for the solution to which the given solution component belongs.
Type: line
Examples:
| Example | Detail |
|---|---|
1 |
|
well solution |
|
solution A |
Category: exptl_crystal_grow_comp
Mandatory: no
The volume of the solution component.
Type: line
Examples:
| Example | Detail |
|---|---|
200 \ml |
|
0.1 ml |
Data items in the GEOM and related (GEOM_ANGLE, GEOM_BOND, GEOM_CONTACT, GEOM_HBOND and GEOM_TORSION) categories record details about the molecular geometry as calculated from the contents of the ATOM, CELL and SYMMETRY data. Geometry data are therefore redundant, in that they can be calculated from other more fundamental quantities in the data block. However, they provide a check on the correctness of both sets of data and enable the most important geometric data to be identified for publication by setting the appropriate publication flag.
Mandatory: no
Keys: _geom.entry_id
Groups: inclusive_group geom_group
Mandatory: yes
This data item is a pointer to _entry.id in the ENTRY category.
Category: geom
Mandatory: no
A description of geometry not covered by the existing data names in the GEOM categories, such as least-squares planes.
Alias: _geom_special_details (cif_core.dic, 2.0.1)
Type: text
Data items in the GEOM_ANGLE category record details about the bond angles as calculated from the contents of the ATOM, CELL and SYMMETRY data.
Mandatory: no
Keys: _geom_angle.atom_site_id_1 _geom_angle.atom_site_id_2 _geom_angle.atom_site_id_3 _geom_angle.site_symmetry_1 _geom_angle.site_symmetry_2 _geom_angle.site_symmetry_3
Groups: inclusive_group geom_group
Examples:
| Example | Detail |
|---|---|
loop_
_geom_angle.atom_site_id_1
_geom_angle.atom_site_id_2
_geom_angle.atom_site_id_3
_geom_angle.value
_geom_angle.value_esd
_geom_angle.site_symmetry_1
_geom_angle.site_symmetry_2
_geom_angle.site_symmetry_3
_geom_angle.publ_flag
C2 O1 C5 111.6 0.2 1_555 1_555 1_555 yes
O1 C2 C3 110.9 0.2 1_555 1_555 1_555 yes
O1 C2 O21 122.2 0.3 1_555 1_555 1_555 yes
C3 C2 O21 127.0 0.3 1_555 1_555 1_555 yes
C2 C3 N4 101.3 0.2 1_555 1_555 1_555 yes
C2 C3 C31 111.3 0.2 1_555 1_555 1_555 yes
C2 C3 H3 107 1 1_555 1_555 1_555 no
N4 C3 C31 116.7 0.2 1_555 1_555 1_555 yes
# - - - - data truncated for brevity - - - -
|
Example 1 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. |
Mandatory: yes
The identifier of the first of the three atom sites that define the angle. This data item is a pointer to _atom_site.id in the ATOM_SITE category.
Alias: _geom_angle_atom_site_label_1 (cif_core.dic, 2.0.1)
Dependent items: _geom_angle.atom_site_id_2 _geom_angle.atom_site_id_3
Mandatory: no
An optional identifier of the first of the three atom sites that define the angle. This data item is a pointer to _atom_site.label_alt_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the first of the three atom sites that define the angle. This data item is a pointer to _atom_site.label_atom_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the first of the three atom sites that define the angle. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the first of the three atom sites that define the angle. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the first of the three atom sites that define the angle. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category.
Mandatory: yes
The identifier of the second of the three atom sites that define the angle. The second atom is taken to be the apex of the angle. This data item is a pointer to _atom_site.id in the ATOM_SITE category.
Alias: _geom_angle_atom_site_label_2 (cif_core.dic, 2.0.1)
Dependent items: _geom_angle.atom_site_id_1 _geom_angle.atom_site_id_3
Mandatory: no
An optional identifier of the second of the three atom sites that define the angle. This data item is a pointer to _atom_site.label_alt_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the second of the three atom sites that define the angle. This data item is a pointer to _atom_site.label_atom_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the second of the three atom sites that define the angle. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the second of the three atom sites that define the angle. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the second of the three atom sites that define the angle. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category.
Mandatory: yes
The identifier of the third of the three atom sites that define the angle. This data item is a pointer to _atom_site.id in the ATOM_SITE category.
Alias: _geom_angle_atom_site_label_3 (cif_core.dic, 2.0.1)
Dependent items: _geom_angle.atom_site_id_1 _geom_angle.atom_site_id_2
Mandatory: no
An optional identifier of the third of the three atom sites that define the angle. This data item is a pointer to _atom_site.label_alt_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the third of the three atom sites that define the angle. This data item is a pointer to _atom_site.label_atom_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the third of the three atom sites that define the angle. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the third of the three atom sites that define the angle. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the third of the three atom sites that define the angle. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the first of the three atom sites that define the angle. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the first of the three atom sites that define the angle. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the first of the three atom sites that define the angle. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the first of the three atom sites that define the angle. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the second of the three atom sites that define the angle. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the second of the three atom sites that define the angle. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the second of the three atom sites that define the angle. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the second of the three atom sites that define the angle. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the third of the three atom sites that define the angle. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the third of the three atom sites that define the angle. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the third of the three atom sites that define the angle. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the third of the three atom sites that define the angle. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category.
Category: geom_angle
Mandatory: no
This code signals whether the angle is referred to in a publication or should be placed in a table of significant angles.
Alias: _geom_angle_publ_flag (cif_core.dic, 2.0.1)
Type: ucode
Enumeration values:
| Value | Detail |
|---|---|
no |
do not include angle in special list |
n |
abbreviation for "no" |
yes |
do include angle in special list |
y |
abbreviation for "yes" |
Category: geom_angle
Mandatory: yes
The symmetry code of the first of the three atom sites that define the angle.
Alias: _geom_angle_site_symmetry_1 (cif_core.dic, 2.0.1)
Type: symop
Default value: 1_555
Examples:
| Example | Detail |
|---|---|
. |
no symmetry or translation to site |
4 |
4th symmetry operation applied |
7_645 |
7th symm. posn.; +a on x; -b on y |
Category: geom_angle
Mandatory: yes
The symmetry code of the second of the three atom sites that define the angle.
Alias: _geom_angle_site_symmetry_2 (cif_core.dic, 2.0.1)
Type: symop
Default value: 1_555
Examples:
| Example | Detail |
|---|---|
. |
no symmetry or translation to site |
4 |
4th symmetry operation applied |
7_645 |
7th symm. posn.; +a on x; -b on y |
Category: geom_angle
Mandatory: yes
The symmetry code of the third of the three atom sites that define the angle.
Alias: _geom_angle_site_symmetry_3 (cif_core.dic, 2.0.1)
Type: symop
Default value: 1_555
Examples:
| Example | Detail |
|---|---|
. |
no symmetry or translation to site |
4 |
4th symmetry operation applied |
7_645 |
7th symm. posn.; +a on x; -b on y |
Category: geom_angle
Mandatory: no
Angle in degrees defined by the three sites _geom_angle.atom_site_id_1, _geom_angle.atom_site_id_2 and _geom_angle.atom_site_id_3.
Alias: _geom_angle (cif_core.dic, 2.0.1)
Type: float
Type conditions: esd
Units: degrees
Related item: _geom_angle.value_esd (associated_esd)
Category: geom_angle
Mandatory: no
The standard uncertainty (estimated standard deviation) of _geom_angle.value.
Type: float
Units: degrees
Related item: _geom_angle.value (associated_value)
Data items in the GEOM_BOND category record details about the bond lengths as calculated from the contents of the ATOM, CELL and SYMMETRY data.
Mandatory: no
Keys: _geom_bond.atom_site_id_1 _geom_bond.atom_site_id_2 _geom_bond.site_symmetry_1 _geom_bond.site_symmetry_2
Groups: inclusive_group geom_group
Examples:
| Example | Detail |
|---|---|
loop_
_geom_bond.atom_site_id_1
_geom_bond.atom_site_id_2
_geom_bond.dist
_geom_bond.dist_esd
_geom_bond.site_symmetry_1
_geom_bond.site_symmetry_2
_geom_bond.publ_flag
O1 C2 1.342 0.004 1_555 1_555 yes
O1 C5 1.439 0.003 1_555 1_555 yes
C2 C3 1.512 0.004 1_555 1_555 yes
C2 O21 1.199 0.004 1_555 1_555 yes
C3 N4 1.465 0.003 1_555 1_555 yes
C3 C31 1.537 0.004 1_555 1_555 yes
C3 H3 1.00 0.03 1_555 1_555 no
N4 C5 1.472 0.003 1_555 1_555 yes
# - - - - data truncated for brevity - - - -
|
Example 1 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. |
Mandatory: yes
The identifier of the first of the two atom sites that define the bond. This data item is a pointer to _atom_site.id in the ATOM_SITE category.
Alias: _geom_bond_atom_site_label_1 (cif_core.dic, 2.0.1)
Dependent item: _geom_bond.atom_site_id_2
Mandatory: no
An optional identifier of the first of the two atom sites that define the bond. This data item is a pointer to _atom_site.label_alt_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the first of the two atom sites that define the bond. This data item is a pointer to _atom_site.label_atom_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the first of the two atom sites that define the bond. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the first of the two atom sites that define the bond. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the first of the two atom sites that define the bond. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category.
Mandatory: yes
The identifier of the second of the two atom sites that define the bond. This data item is a pointer to _atom_site.id in the ATOM_SITE category.
Alias: _geom_bond_atom_site_label_2 (cif_core.dic, 2.0.1)
Dependent item: _geom_bond.atom_site_id_1
Mandatory: no
An optional identifier of the second of the two atom sites that define the bond. This data item is a pointer to _atom_site.label_alt_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the second of the two atom sites that define the bond. This data item is a pointer to _atom_site.label_atom_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the second of the two atom sites that define the bond. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the second of the two atom sites that define the bond. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the second of the two atom sites that define the bond. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the first of the two atom sites that define the bond. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the first of the two atom sites that define the bond. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the first of the two atom sites that define the bond. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the first of the two atom sites that define the bond. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the second of the two atom sites that define the bond. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the second of the two atom sites that define the bond. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the second of the two atom sites that define the bond. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the second of the two atom sites that define the bond. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category.
Category: geom_bond
Mandatory: no
The intramolecular bond distance in angstroms.
Alias: _geom_bond_distance (cif_core.dic, 2.0.1)
Type: float
Type conditions: esd
Units: angstroms
Related item: _geom_bond.dist_esd (associated_esd)
Range: [0.0, .] [0.0, 0.0]
Category: geom_bond
Mandatory: no
The standard uncertainty (estimated standard deviation) of _geom_bond.dist.
Type: float
Units: angstroms
Related item: _geom_bond.dist (associated_value)
Category: geom_bond
Mandatory: no
This code signals whether the bond distance is referred to in a publication or should be placed in a list of significant bond distances.
Alias: _geom_bond_publ_flag (cif_core.dic, 2.0.1)
Type: ucode
Enumeration values:
| Value | Detail |
|---|---|
no |
do not include bond in special list |
n |
abbreviation for "no" |
yes |
do include bond in special list |
y |
abbreviation for "yes" |
Category: geom_bond
Mandatory: yes
The symmetry code of the first of the two atom sites that define the bond.
Alias: _geom_bond_site_symmetry_1 (cif_core.dic, 2.0.1)
Type: symop
Default value: 1_555
Examples:
| Example | Detail |
|---|---|
. |
no symmetry or translation to site |
4 |
4th symmetry operation applied |
7_645 |
7th symm. posn.; +a on x; -b on y |
Category: geom_bond
Mandatory: yes
The symmetry code of the second of the two atom sites that define the bond.
Alias: _geom_bond_site_symmetry_2 (cif_core.dic, 2.0.1)
Type: symop
Default value: 1_555
Examples:
| Example | Detail |
|---|---|
. |
no symmetry or translation to site |
4 |
4th symmetry operation applied |
7_645 |
7th symm. posn.; +a on x; -b on y |
Data items in the GEOM_CONTACT category record details about interatomic contacts as calculated from the contents of the ATOM, CELL and SYMMETRY data.
Mandatory: no
Keys: _geom_contact.atom_site_id_1 _geom_contact.atom_site_id_2 _geom_contact.site_symmetry_1 _geom_contact.site_symmetry_2
Groups: inclusive_group geom_group
Examples:
| Example | Detail |
|---|---|
loop_
_geom_contact.atom_site_id_1
_geom_contact.atom_site_id_2
_geom_contact.dist
_geom_contact.dist_esd
_geom_contact.site_symmetry_1
_geom_contact.site_symmetry_2
_geom_contact.publ_flag
O(1) O(2) 2.735 0.003 . . yes
H(O1) O(2) 1.82 . . . no
|
Example 1 - based on data set CLPHO6 of Ferguson, Ruhl, McKervey & Browne [Acta Cryst. (1992), C48, 2262-2264]. |
Mandatory: yes
The identifier of the first of the two atom sites that define the contact. This data item is a pointer to _atom_site.id in the ATOM_SITE category.
Alias: _geom_contact_atom_site_label_1 (cif_core.dic, 2.0.1)
Dependent item: _geom_contact.atom_site_id_2
Mandatory: no
An optional identifier of the first of the two atom sites that define the contact. This data item is a pointer to _atom_site.label_alt_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the first of the two atom sites that define the contact. This data item is a pointer to _atom_site.label_atom_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the first of the two atom sites that define the contact. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the first of the two atom sites that define the contact. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the first of the two atom sites that define the contact. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category.
Mandatory: yes
The identifier of the second of the two atom sites that define the contact. This data item is a pointer to _atom_site.id in the ATOM_SITE category.
Alias: _geom_contact_atom_site_label_2 (cif_core.dic, 2.0.1)
Dependent item: _geom_contact.atom_site_id_1
Mandatory: no
An optional identifier of the second of the two atom sites that define the contact. This data item is a pointer to _atom_site.label_alt_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the second of the two atom sites that define the contact. This data item is a pointer to _atom_site.label_atom_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the second of the two atom sites that define the contact. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the second of the two atom sites that define the contact. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the second of the two atom sites that define the contact. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the first of the two atom sites that define the contact. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the first of the two atom sites that define the contact. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the first of the two atom sites that define the contact. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the first of the two atom sites that define the contact. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the second of the two atom sites that define the contact. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the second of the two atom sites that define the contact. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the second of the two atom sites that define the contact. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the second of the two atom sites that define the contact. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category.
Category: geom_contact
Mandatory: no
The interatomic contact distance in angstroms.
Alias: _geom_contact_distance (cif_core.dic, 2.0.1)
Type: float
Type conditions: esd
Units: angstroms
Related item: _geom_contact.dist_esd (associated_esd)
Range: [0.0, .] [0.0, 0.0]
Category: geom_contact
Mandatory: no
The standard uncertainty (estimated standard deviation) of _geom_contact.dist.
Type: float
Units: angstroms
Related item: _geom_contact.dist (associated_value)
Category: geom_contact
Mandatory: no
This code signals whether the contact distance is referred to in a publication or should be placed in a list of significant contact distances.
Alias: _geom_contact_publ_flag (cif_core.dic, 2.0.1)
Type: ucode
Enumeration values:
| Value | Detail |
|---|---|
no |
do not include distance in special list |
n |
abbreviation for "no" |
yes |
do include distance in special list |
y |
abbreviation for "yes" |
Category: geom_contact
Mandatory: yes
The symmetry code of the first of the two atom sites that define the contact.
Alias: _geom_contact_site_symmetry_1 (cif_core.dic, 2.0.1)
Type: symop
Default value: 1_555
Examples:
| Example | Detail |
|---|---|
. |
no symmetry or translation to site |
4 |
4th symmetry operation applied |
7_645 |
7th symm. posn.; +a on x; -b on y |
Category: geom_contact
Mandatory: yes
The symmetry code of the second of the two atom sites that define the contact.
Alias: _geom_contact_site_symmetry_2 (cif_core.dic, 2.0.1)
Type: symop
Default value: 1_555
Examples:
| Example | Detail |
|---|---|
. |
no symmetry or translation to site |
4 |
4th symmetry operation applied |
7_645 |
7th symm. posn.; +a on x; -b on y |
Data items in the GEOM_HBOND category record details about hydrogen bonds as calculated from the contents of the ATOM, CELL and SYMMETRY data.
Mandatory: no
Keys: _geom_hbond.atom_site_id_A _geom_hbond.atom_site_id_D _geom_hbond.atom_site_id_H _geom_hbond.site_symmetry_A _geom_hbond.site_symmetry_D _geom_hbond.site_symmetry_H
Groups: inclusive_group geom_group
Examples:
| Example | Detail |
|---|---|
loop_
_geom_hbond.atom_site_id_D
_geom_hbond.atom_site_id_H
_geom_hbond.atom_site_id_A
_geom_hbond.dist_DH
_geom_hbond.dist_HA
_geom_hbond.dist_DA
_geom_hbond.angle_DHA
_geom_hbond.publ_flag
N6 HN6 OW 0.888 1.921 2.801 169.6 yes
OW HO2 O7 0.917 1.923 2.793 153.5 yes
OW HO1 N10 0.894 1.886 2.842 179.7 yes
|
Example 1 - based on C~14~H~13~ClN~2~O.H~2~O, reported by Palmer, Puddle & Lisgarten [Acta Cryst. (1993), C49, 1777-1779]. |
Category: geom_hbond
Mandatory: no
The angle in degrees defined by the donor-, hydrogen- and acceptor-atom sites in a hydrogen bond.
Alias: _geom_hbond_angle_DHA (cif_core.dic, 2.0.1)
Type: float
Type conditions: esd
Units: angstroms
Related item: _geom_hbond.angle_DHA_esd (associated_esd)
Range: [0.0, .] [0.0, 0.0]
Category: geom_hbond
Mandatory: no
The standard uncertainty (estimated standard deviation) of _geom_hbond.angle_DHA.
Type: float
Units: angstroms
Related item: _geom_hbond.angle_DHA (associated_value)
Mandatory: yes
The identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.id in the ATOM_SITE category.
Alias: _geom_hbond_atom_site_label_A (cif_core.dic, 2.0.1)
Dependent items: _geom_hbond.atom_site_id_D _geom_hbond.atom_site_id_H
Mandatory: no
An optional identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.label_alt_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.label_atom_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category.
Mandatory: yes
The identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.id in the ATOM_SITE category.
Alias: _geom_hbond_atom_site_label_D (cif_core.dic, 2.0.1)
Dependent items: _geom_hbond.atom_site_id_A _geom_hbond.atom_site_id_H
Mandatory: no
An optional identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.label_alt_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.label_atom_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category.
Mandatory: yes
The identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.id in the ATOM_SITE category.
Alias: _geom_hbond_atom_site_label_H (cif_core.dic, 2.0.1)
Dependent items: _geom_hbond.atom_site_id_A _geom_hbond.atom_site_id_D
Mandatory: no
An optional identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.label_alt_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.label_atom_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category.
Category: geom_hbond
Mandatory: no
The distance in angstroms between the donor- and acceptor-atom sites in a hydrogen bond.
Alias: _geom_hbond_distance_DA (cif_core.dic, 2.0.1)
Type: float
Type conditions: esd
Units: angstroms
Related item: _geom_hbond.dist_DA_esd (associated_esd)
Range: [0.0, .] [0.0, 0.0]
Category: geom_hbond
Mandatory: no
The standard uncertainty (estimated standard deviation) in angstroms of _geom_hbond.dist_DA.
Type: float
Units: angstroms
Related item: _geom_hbond.dist_DH (associated_value)
Category: geom_hbond
Mandatory: no
The distance in angstroms between the donor- and hydrogen-atom sites in a hydrogen bond.
Alias: _geom_hbond_distance_DH (cif_core.dic, 2.0.1)
Type: float
Type conditions: esd
Units: angstroms
Related item: _geom_hbond.dist_DH_esd (associated_esd)
Range: [0.0, .] [0.0, 0.0]
Category: geom_hbond
Mandatory: no
The standard uncertainty (estimated standard deviation) in angstroms of _geom_hbond.dist_DH.
Type: float
Units: angstroms
Related item: _geom_hbond.dist_DH (associated_value)
Category: geom_hbond
Mandatory: no
The distance in angstroms between the hydrogen- and acceptor- atom sites in a hydrogen bond.
Alias: _geom_hbond_distance_HA (cif_core.dic, 2.0.1)
Type: float
Type conditions: esd
Units: angstroms
Related item: _geom_hbond.dist_HA_esd (associated_esd)
Range: [0.0, .] [0.0, 0.0]
Category: geom_hbond
Mandatory: no
The standard uncertainty (estimated standard deviation) in angstroms of _geom_hbond.dist_HA.
Type: float
Units: angstroms
Related item: _geom_hbond.dist_HA (associated_value)
Category: geom_hbond
Mandatory: no
This code signals whether the hydrogen-bond information is referred to in a publication or should be placed in a table of significant hydrogen-bond geometry.
Alias: _geom_hbond_publ_flag (cif_core.dic, 2.0.1)
Type: ucode
Enumeration values:
| Value | Detail |
|---|---|
no |
do not include bond in special list |
n |
abbreviation for "no" |
yes |
do include bond in special list |
y |
abbreviation for "yes" |
Category: geom_hbond
Mandatory: yes
The symmetry code of the acceptor-atom site that defines the hydrogen bond.
Alias: _geom_hbond_site_symmetry_A (cif_core.dic, 2.0.1)
Type: symop
Default value: 1_555
Examples:
| Example | Detail |
|---|---|
. |
no symmetry or translation to site |
4 |
4th symmetry operation applied |
7_645 |
7th symm. posn.; +a on x; -b on y |
Category: geom_hbond
Mandatory: yes
The symmetry code of the donor-atom site that defines the hydrogen bond.
Alias: _geom_hbond_site_symmetry_D (cif_core.dic, 2.0.1)
Type: symop
Default value: 1_555
Examples:
| Example | Detail |
|---|---|
. |
no symmetry or translation to site |
4 |
4th symmetry operation applied |
7_645 |
7th symm. posn.; +a on x; -b on y |
Category: geom_hbond
Mandatory: yes
The symmetry code of the hydrogen-atom site that defines the hydrogen bond.
Alias: _geom_hbond_site_symmetry_H (cif_core.dic, 2.0.1)
Type: symop
Default value: 1_555
Examples:
| Example | Detail |
|---|---|
. |
no symmetry or translation to site |
4 |
4th symmetry operation applied |
7_645 |
7th symm. posn.; +a on x; -b on y |
Data items in the GEOM_TORSION category record details about torsion angles as calculated from the contents of the ATOM, CELL and SYMMETRY data. The vector direction _geom_torsion.atom_site_id_2 to _geom_torsion.atom_site_id_3 is the viewing direction, and the torsion angle is the angle of twist required to superimpose the projection of the vector between site 2 and site 1 onto the projection of the vector between site 3 and site 4. Clockwise torsions are positive, anticlockwise torsions are negative. Ref: Klyne, W. & Prelog, V. (1960). Experientia, 16, 521-523.
Mandatory: no
Keys: _geom_torsion.atom_site_id_1 _geom_torsion.atom_site_id_2 _geom_torsion.atom_site_id_3 _geom_torsion.atom_site_id_4 _geom_torsion.site_symmetry_1 _geom_torsion.site_symmetry_2 _geom_torsion.site_symmetry_3 _geom_torsion.site_symmetry_4
Groups: inclusive_group geom_group
Examples:
| Example | Detail |
|---|---|
loop_
_geom_torsion.atom_site_id_1
_geom_torsion.atom_site_id_2
_geom_torsion.atom_site_id_3
_geom_torsion.atom_site_id_4
_geom_torsion.value
_geom_torsion.site_symmetry_1
_geom_torsion.site_symmetry_2
_geom_torsion.site_symmetry_3
_geom_torsion.site_symmetry_4
_geom_torsion.publ_flag
C(9) O(2) C(7) C(2) 71.8 . . . . yes
C(7) O(2) C(9) C(10) -168.0 . . . 2_666 yes
C(10) O(3) C(8) C(6) -167.7 . . . . yes
C(8) O(3) C(10) C(9) -69.7 . . . 2_666 yes
O(1) C(1) C(2) C(3) -179.5 . . . . no
O(1) C(1) C(2) C(7) -0.6 . . . . no
|
Example 1 - based on data set CLPHO6 of Ferguson, Ruhl, McKervey & Browne [Acta Cryst. (1992), C48, 2262-2264]. |
Mandatory: yes
The identifier of the first of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.id in the ATOM_SITE category.
Alias: _geom_torsion_atom_site_label_1 (cif_core.dic, 2.0.1)
Dependent items: _geom_torsion.atom_site_id_2 _geom_torsion.atom_site_id_3 _geom_torsion.atom_site_id_4
Mandatory: no
An optional identifier of the first of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.label_alt_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the first of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.label_atom_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the first of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the first of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the first of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category.
Mandatory: yes
The identifier of the second of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.id in the ATOM_SITE category.
Alias: _geom_torsion_atom_site_label_2 (cif_core.dic, 2.0.1)
Dependent items: _geom_torsion.atom_site_id_1 _geom_torsion.atom_site_id_3 _geom_torsion.atom_site_id_4
Mandatory: no
An optional identifier of the second of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.label_alt_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the second of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.label_atom_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the second of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the second of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the second of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category.
Mandatory: yes
The identifier of the third of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.id in the ATOM_SITE category.
Alias: _geom_torsion_atom_site_label_3 (cif_core.dic, 2.0.1)
Dependent items: _geom_torsion.atom_site_id_1 _geom_torsion.atom_site_id_2 _geom_torsion.atom_site_id_4
Mandatory: no
An optional identifier of the third of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.label_alt_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the third of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.label_atom_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the third of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the third of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the third of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category.
Mandatory: yes
The identifier of the fourth of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.id in the ATOM_SITE category.
Alias: _geom_torsion_atom_site_label_4 (cif_core.dic, 2.0.1)
Dependent items: _geom_torsion.atom_site_id_1 _geom_torsion.atom_site_id_2 _geom_torsion.atom_site_id_3
Mandatory: no
An optional identifier of the fourth of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.label_alt_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the fourth of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.label_atom_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the fourth of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the fourth of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the fourth of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the first of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the first of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the first of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the first of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the second of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the second of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the second of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the second of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the third of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the third of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the third of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the third of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the fourth of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the fourth of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the fourth of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category.
Mandatory: no
An optional identifier of the fourth of the four atom sites that define the torsion angle. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category.
Category: geom_torsion
Mandatory: no
This code signals whether the torsion angle is referred to in a publication or should be placed in a table of significant torsion angles.
Alias: _geom_torsion_publ_flag (cif_core.dic, 2.0.1)
Type: ucode
Enumeration values:
| Value | Detail |
|---|---|
no |
do not include angle in special list |
n |
abbreviation for "no" |
yes |
do include angle in special list |
y |
abbreviation for "yes" |
Category: geom_torsion
Mandatory: yes
The symmetry code of the first of the four atom sites that define the torsion angle.
Alias: _geom_torsion_site_symmetry_1 (cif_core.dic, 2.0.1)
Type: symop
Default value: 1_555
Examples:
| Example | Detail |
|---|---|
. |
no symmetry or translation to site |
4 |
4th symmetry operation applied |
7_645 |
7th symm. posn.; +a on x; -b on y |
Category: geom_torsion
Mandatory: yes
The symmetry code of the second of the four atom sites that define the torsion angle.
Alias: _geom_torsion_site_symmetry_2 (cif_core.dic, 2.0.1)
Type: symop
Default value: 1_555
Examples:
| Example | Detail |
|---|---|
. |
no symmetry or translation to site |
4 |
4th symmetry operation applied |
7_645 |
7th symm. posn.; +a on x; -b on y |
Category: geom_torsion
Mandatory: yes
The symmetry code of the third of the four atom sites that define the torsion angle.
Alias: _geom_torsion_site_symmetry_3 (cif_core.dic, 2.0.1)
Type: symop
Default value: 1_555
Examples:
| Example | Detail |
|---|---|
. |
no symmetry or translation to site |
4 |
4th symmetry operation applied |
7_645 |
7th symm. posn.; +a on x; -b on y |
Category: geom_torsion
Mandatory: yes
The symmetry code of the fourth of the four atom sites that define the torsion angle.
Alias: _geom_torsion_site_symmetry_4 (cif_core.dic, 2.0.1)
Type: symop
Default value: 1_555
Examples:
| Example | Detail |
|---|---|
. |
no symmetry or translation to site |
4 |
4th symmetry operation applied |
7_645 |
7th symm. posn.; +a on x; -b on y |
Category: geom_torsion
Mandatory: no
The value of the torsion angle in degrees.
Alias: _geom_torsion (cif_core.dic, 2.0.1)
Type: float
Type conditions: esd
Units: degrees
Related item: _geom_torsion.value_esd (associated_esd)
Category: geom_torsion
Mandatory: no
The standard uncertainty (estimated standard deviation) of _geom_torsion.value.
Type: float
Units: degrees
Related item: _geom_torsion.value (associated_value)
Data items in the JOURNAL category record details about the book-keeping by the journal staff when processing a data block submitted for publication. The creator of a data block will not normally specify these data. The data names are not defined in the dictionary because they are for journal use only.
Mandatory: no
Keys: _journal.entry_id
Groups: inclusive_group iucr_group
Examples:
| Example | Detail |
|---|---|
_journal.entry_id 'TOZ'
_journal.date_recd_electronic 1991-04-15
_journal.date_from_coeditor 1991-04-18
_journal.date_accepted 1991-04-18
_journal.date_printers_first 1991-08-07
_journal.date_proofs_out 1991-08-07
_journal.coeditor_code HL0007
_journal.techeditor_code C910963
_journal.coden_ASTM ACSCEE
_journal.name_full 'Acta Crystallographica Section C'
_journal.year 1991
_journal.volume 47
_journal.issue NOV91
_journal.page_first 2276
_journal.page_last 2277
|
Example 1 - based on Acta Cryst. file for entry HL0007 [Willis, Beckwith & Tozer (1991). Acta Cryst. C47, 2276-2277]. |
Mandatory: yes
This data item is a pointer to _entry.id in the ENTRY category.
Category: journal
Mandatory: no
Journal data items are defined by the journal staff.
Alias: _journal_coden_ASTM (cif_core.dic, 2.0.1)
Type: line
Category: journal
Mandatory: no
Journal data items are defined by the journal staff.
Alias: _journal_coden_Cambridge (cif_core.dic, 2.0.1)
Type: line
Category: journal
Mandatory: no
Journal data items are defined by the journal staff.
Alias: _journal_coeditor_address (cif_core.dic, 2.0.1)
Type: text
Category: journal
Mandatory: no
Journal data items are defined by the journal staff.
Alias: _journal_coeditor_code (cif_core.dic, 2.0.1)
Type: line
Category: journal
Mandatory: no
Journal data items are defined by the journal staff.
Alias: _journal_coeditor_email (cif_core.dic, 2.0.1)
Type: line
Category: journal
Mandatory: no
Journal data items are defined by the journal staff.
Alias: _journal_coeditor_fax (cif_core.dic, 2.0.1)
Type: line
Category: journal
Mandatory: no
Journal data items are defined by the journal staff.
Alias: _journal_coeditor_name (cif_core.dic, 2.0.1)
Type: line
Category: journal
Mandatory: no
Journal data items are defined by the journal staff.
Alias: _journal_coeditor_notes (cif_core.dic, 2.0.1)
Type: text
Category: journal
Mandatory: no
Journal data items are defined by the journal staff.
Alias: _journal_coeditor_phone (cif_core.dic, 2.0.1)
Type: line
Category: journal
Mandatory: no
Journal data items are defined by the journal staff.
Alias: _journal_data_validation_number (cif_core.dic, 2.0.1)
Type: code
Category: journal
Mandatory: no
Journal data items are defined by the journal staff.
Alias: _journal_date_accepted (cif_core.dic, 2.0.1)
Type: yyyy-mm-dd
Category: journal
Mandatory: no
Journal data items are defined by the journal staff.
Alias: _journal_date_from_coeditor (cif_core.dic, 2.0.1)
Type: yyyy-mm-dd
Category: journal
Mandatory: no
Journal data items are defined by the journal staff.
Alias: _journal_date_to_coeditor (cif_core.dic, 2.0.1)
Type: yyyy-mm-dd
Category: journal
Mandatory: no
Journal data items are defined by the journal staff.
Alias: _journal_date_printers_final (cif_core.dic, 2.0.1)
Type: yyyy-mm-dd
Category: journal
Mandatory: no
Journal data items are defined by the journal staff.
Alias: _journal_date_printers_first (cif_core.dic, 2.0.1)
Type: yyyy-mm-dd
Category: journal
Mandatory: no
Journal data items are defined by the journal staff.
Alias: _journal_date_proofs_in (cif_core.dic, 2.0.1)
Type: yyyy-mm-dd
Category: journal
Mandatory: no
Journal data items are defined by the journal staff.
Alias: _journal_date_proofs_out (cif_core.dic, 2.0.1)
Type: yyyy-mm-dd
Category: journal
Mandatory: no
Journal data items are defined by the journal staff.
Alias: _journal_date_recd_copyright (cif_core.dic, 2.0.1)
Type: yyyy-mm-dd
Category: journal
Mandatory: no
Journal data items are defined by the journal staff.
Alias: _journal_date_recd_electronic (cif_core.dic, 2.0.1)
Type: yyyy-mm-dd
Category: journal
Mandatory: no
Journal data items are defined by the journal staff.
Alias: _journal_date_recd_hard_copy (cif_core.dic, 2.0.1)
Type: yyyy-mm-dd
Category: journal
Mandatory: no
Journal data items are defined by the journal staff.
Alias: _journal_issue (cif_core.dic, 2.0.1)
Type: line
Category: journal
Mandatory: no
Journal data items are defined by the journal staff.
Alias: _journal_language (cif_core.dic, 2.0.1)
Type: line
Category: journal
Mandatory: no
Journal data items are defined by the journal staff.
Alias: _journal_name_full (cif_core.dic, 2.0.1)
Type: line
Category: journal
Mandatory: no
Journal data items are defined by the journal staff.
Alias: _journal_page_first (cif_core.dic, 2.0.1)
Type: line
Category: journal
Mandatory: no
Journal data items are defined by the journal staff.
Alias: _journal_page_last (cif_core.dic, 2.0.1)
Type: line
Category: journal
Mandatory: no
Journal data items are defined by the journal staff.
Alias: _journal_paper_category (cif_core.dic, 2.0.1)
Type: line
Category: journal
Mandatory: no
Journal data items are defined by the journal staff.
Alias: _journal_suppl_publ_number (cif_core.dic, 2.0.1)
Type: line
Category: journal
Mandatory: no
Journal data items are defined by the journal staff.
Alias: _journal_suppl_publ_pages (cif_core.dic, 2.0.1)
Type: line
Category: journal
Mandatory: no
Journal data items are defined by the journal staff.
Alias: _journal_techeditor_address (cif_core.dic, 2.0.1)
Type: text
Category: journal
Mandatory: no
Journal data items are defined by the journal staff.
Alias: _journal_techeditor_code (cif_core.dic, 2.0.1)
Type: line
Category: journal
Mandatory: no
Journal data items are defined by the journal staff.
Alias: _journal_techeditor_email (cif_core.dic, 2.0.1)
Type: line
Category: journal
Mandatory: no
Journal data items are defined by the journal staff.
Alias: _journal_techeditor_fax (cif_core.dic, 2.0.1)
Type: line
Category: journal
Mandatory: no
Journal data items are defined by the journal staff.
Alias: _journal_techeditor_name (cif_core.dic, 2.0.1)
Type: line
Category: journal
Mandatory: no
Journal data items are defined by the journal staff.
Alias: _journal_techeditor_notes (cif_core.dic, 2.0.1)
Type: text
Category: journal
Mandatory: no
Journal data items are defined by the journal staff.
Alias: _journal_techeditor_phone (cif_core.dic, 2.0.1)
Type: line
Category: journal
Mandatory: no
Journal data items are defined by the journal staff.
Alias: _journal_volume (cif_core.dic, 2.0.1)
Type: line
Category: journal
Mandatory: no
Journal data items are defined by the journal staff.
Alias: _journal_year (cif_core.dic, 2.0.1)
Type: line
Data items in the JOURNAL_INDEX category are used to list terms used to generate the journal indexes. The creator of a data block will not normally specify these data items.
Mandatory: no
Keys: _journal_index.type _journal_index.term
Groups: inclusive_group iucr_group
Examples:
| Example | Detail |
|---|---|
loop_
_journal_index.type
_journal_index.term
_journal_index.subterm
O C16H19NO4 .
S alkaloids (-)-norcocaine
S (-)-norcocaine .
S
; [2R,3S-(2\b,3\b)]-methyl
3-(benzoyloxy)-8-azabicyclo[3.2.1]octane-2-carboxylate
;
.
|
Example 1 - based on a paper by Zhu, Reynolds, Klein & Trudell [Acta Cryst. (1994), C50, 2067-2069]. |
Category: journal_index
Mandatory: no
Journal index data items are defined by the journal staff.
Alias: _journal_index_subterm (cif_core.dic, 2.0.1)
Type: line
Category: journal_index
Mandatory: no
Journal index data items are defined by the journal staff.
Alias: _journal_index_term (cif_core.dic, 2.0.1)
Type: line
Category: journal_index
Mandatory: no
Journal index data items are defined by the journal staff.
Alias: _journal_index_type (cif_core.dic, 2.0.1)
Type: line
Data items in the PHASING category record details about the phasing of the structure, listing the various methods used in the phasing process. Details about the application of each method are listed in the appropriate subcategories.
Mandatory: no
Keys: _phasing.method
Groups: inclusive_group phasing_group
Examples:
| Example | Detail |
|---|---|
loop_
_phasing.method
'mir'
'averaging'
|
Example 1 - hypothetical example. |
Category: phasing
Mandatory: yes
A listing of the method or methods used to phase this structure.
Type: ucode
Examples:
| Example | Detail |
|---|---|
abinitio |
phasing by ab initio methods |
averaging |
phase improvement by averaging over multiple images of the structure |
dm |
phasing by direct methods |
isas |
phasing by iterative single-wavelength anomalous scattering |
isir |
phasing by iterative single-wavelength isomorphous replacement |
isomorphous |
phasing beginning with phases calculated from an isomorphous structure |
mad |
phasing by multiple-wavelength anomalous dispersion |
mir |
phasing by multiple isomorphous replacement |
miras |
phasing by multiple isomorphous replacement with anomalous scattering |
mr |
phasing by molecular replacement |
sir |
phasing by single isomorphous replacement |
siras |
phasing by single isomorphous replacement with anomalous scattering |
Data items in the PHASING_AVERAGING category record details about the phasing of the structure where methods involving averaging of multiple observations of the molecule in the asymmetric unit are involved.
Mandatory: no
Keys: _phasing_averaging.entry_id
Groups: inclusive_group phasing_group
Examples:
| Example | Detail |
|---|---|
_phasing_averaging.entry_id 'EXAMHYPO'
_phasing_averaging.method
; Iterative threefold averaging alternating with phase
extensions by 0.5 reciprocal lattice units per cycle.
;
_phasing_averaging.details
; The position of the threefold axis was redetermined every
five cycles.
;
|
Example 1 - hypothetical example. |
Category: phasing_averaging
Mandatory: no
A description of special aspects of the averaging process.
Type: text
Mandatory: yes
This data item is a pointer to _entry.id in the ENTRY category.
Category: phasing_averaging
Mandatory: no
A description of the phase-averaging phasing method used to phase this structure. Note that this is not the computer program used, which is described in the SOFTWARE category, but rather the method itself. This data item should be used to describe significant methodological options used within the phase-averaging program.
Type: text
Data items in the PHASING_ISOMORPHOUS category record details about the phasing of the structure where a model isomorphous to the structure being phased was used to generate the initial phases.
Mandatory: no
Keys: _phasing_isomorphous.entry_id
Groups: inclusive_group phasing_group
Examples:
| Example | Detail |
|---|---|
_phasing_isomorphous.parent 'PDB entry 5HVP'
_phasing_isomorphous.details
; The inhibitor and all solvent atoms were removed from the
parent structure before beginning refinement. All static
disorder present in the parent structure was also removed.
;
|
Example 1 - based on PDB entry 4PHV and laboratory records for the structure corresponding to PDB entry 4PHV. |
Category: phasing_isomorphous
Mandatory: no
A description of special aspects of the isomorphous phasing.
Type: text
Example:
Residues 13-18 were eliminated from the
starting model as it was anticipated that
binding of the inhibitor would cause a
structural rearrangement in this part of the
structure.
Mandatory: yes
This data item is a pointer to _entry.id in the ENTRY category.
Category: phasing_isomorphous
Mandatory: no
A description of the isomorphous-phasing method used to phase this structure. Note that this is not the computer program used, which is described in the SOFTWARE category, but rather the method itself. This data item should be used to describe significant methodological options used within the isomorphous phasing program.
Type: text
Example:
Iterative threefold averaging alternating with
phase extension by 0.5 reciprocal lattice
units per cycle.
Category: phasing_isomorphous
Mandatory: no
Reference to the structure used to generate starting phases if the structure referenced in this data block was phased by virtue of being isomorphous to a known structure (e.g. a mutant that crystallizes in the same space group as the wild-type protein.)
Type: text
Data items in the PHASING_MAD category record details about the phasing of the structure where methods involving multiple-wavelength anomalous-dispersion techniques are involved.
Mandatory: no
Keys: _phasing_MAD.entry_id
Groups: inclusive_group phasing_group
Examples:
| Example | Detail |
|---|---|
_phasing_MAD.entry_id 'NCAD'
|
Example 1 - based on a paper by Shapiro et al. [Nature (London) (1995), 374, 327-337]. |
Category: phasing_MAD
Mandatory: no
A description of special aspects of the MAD phasing.
Type: text
Mandatory: yes
This data item is a pointer to _entry.id in the ENTRY category.
Category: phasing_MAD
Mandatory: no
A description of the MAD phasing method used to phase this structure. Note that this is not the computer program used, which is described in the SOFTWARE category, but rather the method itself. This data item should be used to describe significant methodological options used within the MAD phasing program.
Type: text
Data items in the PHASING_MAD_CLUST category record details about a cluster of experiments that contributed to the generation of a set of phases.
Mandatory: no
Keys: _phasing_MAD_clust.expt_id _phasing_MAD_clust.id
Groups: inclusive_group phasing_group
Examples:
| Example | Detail |
|---|---|
loop_
_phasing_MAD_clust.id
_phasing_MAD_clust.expt_id
_phasing_MAD_clust.number_set
'4 wavelength' 1 4
'5 wavelength' 1 5
'5 wavelength' 2 5
|
Example 1 - based on a paper by Shapiro et al. [Nature (London) (1995), 374, 327-337]. |
Mandatory: yes
This data item is a pointer to _phasing_MAD_expt.id in the PHASING_MAD_EXPT category.
| Name | Category | Mandatory |
|---|---|---|
| _phasing_MAD_clust.id | phasing_MAD_clust | yes |
| _phasing_MAD_set.clust_id | phasing_MAD_set | yes |
| _phasing_MAD_ratio.clust_id | phasing_MAD_ratio | yes |
The value of _phasing_MAD_clust.id must, together with _phasing_MAD_clust.expt_id, uniquely identify a record in the PHASING_MAD_CLUST list. Note that this item need not be a number; it can be any unique identifier.
Type: code
Child / Parent relations:
| Child | Parent |
|---|---|
| _phasing_MAD_set.clust_id | _phasing_MAD_clust.id |
| _phasing_MAD_ratio.clust_id | _phasing_MAD_clust.id |
Category: phasing_MAD_clust
Mandatory: no
The number of data sets in this cluster of data sets.
Type: int
Data items in the PHASING_MAD_EXPT category record details about a MAD phasing experiment, such as the number of experiments that were clustered together to produce a set of phases or the statistics for those phases.
Mandatory: no
Keys: _phasing_MAD_expt.id
Groups: inclusive_group phasing_group
Examples:
| Example | Detail |
|---|---|
loop_
_phasing_MAD_expt.id
_phasing_MAD_expt.number_clust
_phasing_MAD_expt.R_normal_all
_phasing_MAD_expt.R_normal_anom_scat
_phasing_MAD_expt.delta_delta_phi
_phasing_MAD_expt.delta_phi_sigma
_phasing_MAD_expt.mean_fom
1 2 0.063 0.451 58.5 20.3 0.88
2 1 0.051 0.419 36.8 18.2 0.93
|
Example 1 - based on a paper by Shapiro et al. [Nature (London) (1995), 374, 327-337]. |
Category: phasing_MAD_expt
Mandatory: no
The difference between two independent determinations of _phasing_MAD_expt.delta_phi.
Type: float
Category: phasing_MAD_expt
Mandatory: no
The phase difference between Ft(h), the structure factor due to normal scattering from all atoms, and Fa(h), the structure factor due to normal scattering from only the anomalous scatterers.
Type: float
Related item: _phasing_MAD_expt.delta_phi_sigma (associated_esd)
Category: phasing_MAD_expt
Mandatory: no
The standard uncertainty (estimated standard deviation) of _phasing_MAD_expt.delta_phi.
Type: float
Related item: _phasing_MAD_expt.delta_phi (associated_value)
| Name | Category | Mandatory |
|---|---|---|
| _phasing_MAD_expt.id | phasing_MAD_expt | yes |
| _phasing_MAD_clust.expt_id | phasing_MAD_clust | yes |
| _phasing_MAD_set.expt_id | phasing_MAD_set | yes |
| _phasing_MAD_ratio.expt_id | phasing_MAD_ratio | yes |
The value of _phasing_MAD_expt.id must uniquely identify each record in the PHASING_MAD_EXPT list.
Type: code
Child / Parent relations:
| Child | Parent |
|---|---|
| _phasing_MAD_clust.expt_id | _phasing_MAD_expt.id |
| _phasing_MAD_set.expt_id | _phasing_MAD_expt.id |
| _phasing_MAD_ratio.expt_id | _phasing_MAD_expt.id |
Category: phasing_MAD_expt
Mandatory: no
The mean figure of merit.
Type: float
Category: phasing_MAD_expt
Mandatory: no
The number of clusters of data sets in this phasing experiment.
Type: int
Category: phasing_MAD_expt
Mandatory: no
Definition...
Type: float
Data items in the PHASING_MAD_RATIO category record the ratios of phasing statistics between pairs of data sets in a MAD phasing experiment, in given shells of resolution.
Mandatory: no
Keys: _phasing_MAD_ratio.clust_id _phasing_MAD_ratio.expt_id _phasing_MAD_ratio.wavelength_1 _phasing_MAD_ratio.wavelength_2
Groups: inclusive_group phasing_group
Examples:
| Example | Detail |
|---|---|
loop_
_phasing_MAD_ratio.expt_id
_phasing_MAD_ratio.clust_id
_phasing_MAD_ratio.wavelength_1
_phasing_MAD_ratio.wavelength_2
_phasing_MAD_ratio.d_res_low
_phasing_MAD_ratio.d_res_high
_phasing_MAD_ratio.ratio_two_wl
_phasing_MAD_ratio.ratio_one_wl
_phasing_MAD_ratio.ratio_one_wl_centric
1 '4 wavelength' 1.4013 1.4013 20.00 4.00 . 0.084 0.076
1 '4 wavelength' 1.4013 1.3857 20.00 4.00 0.067 . .
1 '4 wavelength' 1.4013 1.3852 20.00 4.00 0.051 . .
1 '4 wavelength' 1.4013 1.3847 20.00 4.00 0.044 . .
1 '4 wavelength' 1.3857 1.3857 20.00 4.00 . 0.110 0.049
1 '4 wavelength' 1.3857 1.3852 20.00 4.00 0.049 . .
1 '4 wavelength' 1.3857 1.3847 20.00 4.00 0.067 . .
1 '4 wavelength' 1.3852 1.3852 20.00 4.00 . 0.149 0.072
1 '4 wavelength' 1.3852 1.3847 20.00 4.00 0.039 . .
1 '4 wavelength' 1.3847 1.3847 20.00 4.00 . 0.102 0.071
1 '4 wavelength' 1.4013 1.4013 4.00 3.00 . 0.114 0.111
1 '4 wavelength' 1.4013 1.3857 4.00 3.00 0.089 . .
1 '4 wavelength' 1.4013 1.3852 4.00 3.00 0.086 . .
1 '4 wavelength' 1.4013 1.3847 4.00 3.00 0.077 . .
1 '4 wavelength' 1.3857 1.3857 4.00 3.00 . 0.140 0.127
1 '4 wavelength' 1.3857 1.3852 4.00 3.00 0.085 . .
1 '4 wavelength' 1.3857 1.3847 4.00 3.00 0.089 . .
1 '4 wavelength' 1.3852 1.3852 4.00 3.00 . 0.155 0.119
1 '4 wavelength' 1.3852 1.3847 4.00 3.00 0.082 . .
1 '4 wavelength' 1.3847 1.3847 4.00 3.00 . 0.124 0.120
1 '5 wavelength' 1.3857 1.3857 20.00 4.00 . 0.075 0.027
1 '5 wavelength' 1.3857 1.3852 20.00 4.00 0.041 . .
1 '5 wavelength' 1.3857 1.3847 20.00 4.00 0.060 . .
1 '5 wavelength' 1.3857 1.3784 20.00 4.00 0.057 . .
1 '5 wavelength' 1.3857 1.2862 20.00 4.00 0.072 . .
1 '5 wavelength' 1.3852 1.3852 20.00 4.00 . 0.105 0.032
1 '5 wavelength' 1.3852 1.3847 20.00 4.00 0.036 . .
1 '5 wavelength' 1.3852 1.3784 20.00 4.00 0.044 . .
1 '5 wavelength' 1.3852 1.2862 20.00 4.00 0.065 . .
1 '5 wavelength' 1.3847 1.3847 20.00 4.00 . 0.072 0.031
1 '5 wavelength' 1.3847 1.3784 20.00 4.00 0.040 . .
1 '5 wavelength' 1.3847 1.2862 20.00 4.00 0.059 . .
1 '5 wavelength' 1.3784 1.3784 20.00 4.00 . 0.059 0.032
1 '5 wavelength' 1.3784 1.2862 20.00 4.00 0.059 . .
1 '5 wavelength' 1.2862 1.3847 20.00 4.00 . 0.058 0.028
1 '5 wavelength' 1.3857 1.3857 4.00 3.00 . 0.078 0.075
1 '5 wavelength' 1.3857 1.3852 4.00 3.00 0.059 . .
1 '5 wavelength' 1.3857 1.3847 4.00 3.00 0.067 . .
1 '5 wavelength' 1.3857 1.3784 4.00 3.00 0.084 . .
1 '5 wavelength' 1.3857 1.2862 4.00 3.00 0.073 . .
1 '5 wavelength' 1.3852 1.3852 4.00 3.00 . 0.101 0.088
1 '5 wavelength' 1.3852 1.3847 4.00 3.00 0.066 . .
1 '5 wavelength' 1.3852 1.3784 4.00 3.00 0.082 . .
1 '5 wavelength' 1.3852 1.2862 4.00 3.00 0.085 . .
1 '5 wavelength' 1.3847 1.3847 4.00 3.00 . 0.097 0.074
1 '5 wavelength' 1.3847 1.3784 4.00 3.00 0.081 . .
1 '5 wavelength' 1.3847 1.2862 4.00 3.00 0.085 . .
1 '5 wavelength' 1.3784 1.3784 4.00 3.00 . 0.114 0.089
1 '5 wavelength' 1.3784 1.2862 4.00 3.00 0.103 . .
1 '5 wavelength' 1.2862 1.2862 4.00 3.00 . 0.062 0.060
2 '5 wavelength' 0.7263 0.7263 15.00 3.00 . 0.035 0.026
2 '5 wavelength' 0.7263 0.7251 15.00 3.00 0.028 . .
2 '5 wavelength' 0.7263 0.7284 15.00 3.00 0.023 . .
2 '5 wavelength' 0.7263 0.7246 15.00 3.00 0.025 . .
2 '5 wavelength' 0.7263 0.7217 15.00 3.00 0.026 . .
2 '5 wavelength' 0.7251 0.7251 15.00 3.00 . 0.060 0.026
2 '5 wavelength' 0.7251 0.7284 15.00 3.00 0.029 . .
2 '5 wavelength' 0.7251 0.7246 15.00 3.00 0.031 . .
2 '5 wavelength' 0.7251 0.7217 15.00 3.00 0.035 . .
2 '5 wavelength' 0.7284 0.7284 15.00 3.00 . 0.075 0.030
2 '5 wavelength' 0.7284 0.7246 15.00 3.00 0.023 . .
2 '5 wavelength' 0.7284 0.7217 15.00 3.00 0.027 . .
2 '5 wavelength' 0.7246 0.7246 15.00 3.00 . 0.069 0.026
2 '5 wavelength' 0.7246 0.7217 15.00 3.00 0.024 . .
2 '5 wavelength' 0.7217 0.7284 15.00 3.00 . 0.060 0.028
2 '5 wavelength' 0.7263 0.7263 3.00 1.90 . 0.060 0.050
2 '5 wavelength' 0.7263 0.7251 3.00 1.90 0.056 . .
2 '5 wavelength' 0.7263 0.7284 3.00 1.90 0.055 . .
2 '5 wavelength' 0.7263 0.7246 3.00 1.90 0.053 . .
2 '5 wavelength' 0.7263 0.7217 3.00 1.90 0.056 . .
2 '5 wavelength' 0.7251 0.7251 3.00 1.90 . 0.089 0.050
2 '5 wavelength' 0.7251 0.7284 3.00 1.90 0.054 . .
2 '5 wavelength' 0.7251 0.7246 3.00 1.90 0.058 . .
2 '5 wavelength' 0.7251 0.7217 3.00 1.90 0.063 . .
2 '5 wavelength' 0.7284 0.7284 3.00 1.90 . 0.104 0.057
2 '5 wavelength' 0.7284 0.7246 3.00 1.90 0.052 . .
2 '5 wavelength' 0.7284 0.7217 3.00 1.90 0.057 . .
2 '5 wavelength' 0.7246 0.7246 3.00 1.90 . 0.098 0.052
2 '5 wavelength' 0.7246 0.7217 3.00 1.90 0.054 . .
2 '5 wavelength' 0.7217 0.7284 3.00 1.90 . 0.089 0.060
|
Example 1 - based on a paper by Shapiro et al. [Nature (London) (1995), 374, 327-337]. |
Category: phasing_MAD_ratio
Mandatory: no
The lowest value for the interplanar spacings for the reflection data used for the comparison of Bijvoet differences. This is called the highest resolution.
Type: float
Category: phasing_MAD_ratio
Mandatory: no
The highest value for the interplanar spacings for the reflection data used for the comparison of Bijvoet differences. This is called the lowest resolution.
Type: float
Mandatory: yes
This data item is a pointer to _phasing_MAD_expt.id in the PHASING_MAD_EXPT category.
Mandatory: yes
This data item is a pointer to _phasing_MAD_clust.id in the PHASING_MAD_CLUST category.
Category: phasing_MAD_ratio
Mandatory: no
The root-mean-square Bijvoet difference at one wavelength for all reflections.
Type: float
Category: phasing_MAD_ratio
Mandatory: no
The root-mean-square Bijvoet difference at one wavelength for centric reflections. This would be equal to zero for perfect data and thus serves as an estimate of the noise in the anomalous signals.
Type: float
Category: phasing_MAD_ratio
Mandatory: no
The root-mean-square dispersive Bijvoet difference between two wavelengths for all reflections.
Type: float
Mandatory: yes
This data item is a pointer to _phasing_MAD_set.wavelength in the PHASING_MAD_SET category.
Mandatory: yes
This data item is a pointer to _phasing_MAD_set.wavelength in the PHASING_MAD_SET category.
Data items in the PHASING_MAD_SET category record details about the individual data sets used in a MAD phasing experiment.
Mandatory: no
Keys: _phasing_MAD_set.expt_id _phasing_MAD_set.clust_id _phasing_MAD_set.set_id _phasing_MAD_set.wavelength
Groups: inclusive_group phasing_group
Examples:
| Example | Detail |
|---|---|
loop_
_phasing_MAD_set.expt_id
_phasing_MAD_set.clust_id
_phasing_MAD_set.set_id
_phasing_MAD_set.wavelength
_phasing_MAD_set.wavelength_details
_phasing_MAD_set.d_res_low
_phasing_MAD_set.d_res_high
_phasing_MAD_set.f_prime
_phasing_MAD_set.f_double_prime
1 '4 wavelength' aa 1.4013 'pre-edge' 20.00 3.00
-12.48 3.80
1 '4 wavelength' bb 1.3857 'peak' 20.00 3.00
-31.22 17.20
1 '4 wavelength' cc 1.3852 'edge' 20.00 3.00
-13.97 29.17
1 '4 wavelength' dd 1.3847 'remote' 20.00 3.00
-6.67 17.34
1 '5 wavelength' ee 1.3857 'ascending edge' 20.00 3.00
-28.33 14.84
1 '5 wavelength' ff 1.3852 'peak' 20.00 3.00
-21.50 30.23
1 '5 wavelength' gg 1.3847 'descending edge' 20.00 3.00
-10.71 20.35
1 '5 wavelength' hh 1.3784 'remote 1' 20.00 3.00
-14.45 11.84
1 '5 wavelength' ii 1.2862 'remote 2' 20.00 3.00
-9.03 9.01
2 '5 wavelength' jj 0.7263 'pre-edge' 15.00 1.90
-21.10 4.08
2 '5 wavelength' kk 0.7251 'edge' 15.00 1.90
-34.72 7.92
2 '5 wavelength' ll 0.7248 'peak' 15.00 1.90
-24.87 10.30
2 '5 wavelength' mm 0.7246 'descending edge' 15.00 1.90
-17.43 9.62
2 '5 wavelength' nn 0.7217 'remote' 15.00 1.90
-13.26 8.40
|
Example 1 - based on a paper by Shapiro et al. [Nature (London) (1995), 374, 327-337]. |
Mandatory: yes
This data item is a pointer to _phasing_MAD_clust.id in the PHASING_MAD_CLUST category.
Category: phasing_MAD_set
Mandatory: no
The lowest value for the interplanar spacings for the reflection data used for this set of data. This is called the highest resolution.
Type: float
Category: phasing_MAD_set
Mandatory: no
The highest value for the interplanar spacings for the reflection data used for this set of data. This is called the lowest resolution.
Type: float
Mandatory: yes
This data item is a pointer to _phasing_MAD_expt.id in the PHASING_MAD_EXPT category.
Category: phasing_MAD_set
Mandatory: no
The f'' component of the anomalous scattering factor for this wavelength.
Type: float
Category: phasing_MAD_set
Mandatory: no
The f' component of the anomalous scattering factor for this wavelength.
Type: float
Mandatory: yes
This data item is a pointer to _phasing_set.id in the PHASING_SET category.
| Name | Category | Mandatory |
|---|---|---|
| _phasing_MAD_set.wavelength | phasing_MAD_set | yes |
| _phasing_MAD_ratio.wavelength_1 | phasing_MAD_ratio | yes |
| _phasing_MAD_ratio.wavelength_2 | phasing_MAD_ratio | yes |
The wavelength at which this data set was measured.
Type: float
Child / Parent relations:
| Child | Parent |
|---|---|
| _phasing_MAD_ratio.wavelength_1 | _phasing_MAD_set.wavelength |
| _phasing_MAD_ratio.wavelength_2 | _phasing_MAD_set.wavelength |
Category: phasing_MAD_set
Mandatory: no
A descriptor for this wavelength in this cluster of data sets.
Type: text
Examples:
| Example | Detail |
|---|---|
peak |
|
remote |
|
ascending edge |
Data items in the PHASING_MIR category record details about the phasing of the structure where methods involving isomorphous replacement are involved. All isomorphous-replacement-based techniques are covered by this category, including single isomorphous replacement (SIR), multiple isomorphous replacement (MIR) and single or multiple isomorphous replacement plus anomalous scattering (SIRAS, MIRAS).
Mandatory: no
Keys: _phasing_MIR.entry_id
Groups: inclusive_group phasing_group
Examples:
| Example | Detail |
|---|---|
_phasing_MIR.method
; Standard phase refinement (Blow & Crick, 1959)
;
|
Example 1 - based on a paper by Zanotti et al. [J. Biol. Chem. (1993), 268, 10728-10738]. |
Category: phasing_MIR
Mandatory: no
A description of special aspects of the isomorphous-replacement phasing.
Type: text
Category: phasing_MIR
Mandatory: yes
The lowest value in angstroms for the interplanar spacings for the reflection data used for the native data set. This is called the highest resolution.
Alias: _phasing_MIR.ebi_d_res_high (ebi_extensions, 1.0)
Type: float
Units: angstroms
Range: [0.0, .] [0.0, 0.0]
Category: phasing_MIR
Mandatory: yes
The highest value in angstroms for the interplanar spacings for the reflection data used for the native data set. This is called the lowest resolution.
Alias: _phasing_MIR.ebi_d_res_low (ebi_extensions, 1.0)
Type: float
Units: angstroms
Range: [0.0, .] [0.0, 0.0]
Mandatory: yes
This data item is a pointer to _entry.id in the ENTRY category.
Category: phasing_MIR
Mandatory: no
The mean value of the figure of merit m for all reflections phased in the native data set. int Palpha exp(i*alpha) dalpha m = -------------------------------- int Palpha dalpha Pa = the probability that the phase angle a is correct the integral is taken over the range alpha = 0 to 2 pi.
Alias: _phasing_MIR.ebi_fom (ebi_extensions, 1.0)
Type: float
Range: [0.0, .] [0.0, 0.0]
Category: phasing_MIR
Mandatory: no
The mean value of the figure of merit m for the acentric reflections phased in the native data set. int Palpha exp(i*alpha) dalpha m = -------------------------------- int Palpha dalpha Pa = the probability that the phase angle a is correct the integral is taken over the range alpha = 0 to 2 pi.
Alias: _phasing_MIR.ebi_fom_acentric (ebi_extensions, 1.0)
Type: float
Range: [0.0, .] [0.0, 0.0]
Category: phasing_MIR
Mandatory: no
The mean value of the figure of merit m for the centric reflections phased in the native data set. int Palpha exp(i*alpha) dalpha m = -------------------------------- int Palpha dalpha Pa = the probability that the phase angle a is correct the integral is taken over the range alpha = 0 to 2 pi.
Alias: _phasing_MIR.ebi_fom_centric (ebi_extensions, 1.0)
Type: float
Range: [0.0, .] [0.0, 0.0]
Category: phasing_MIR
Mandatory: no
A description of the MIR phasing method applied to phase this structure. Note that this is not the computer program used, which is described in the SOFTWARE category, but rather the method itself. This data item should be used to describe significant methodological options used within the MIR phasing program.
Type: text
Category: phasing_MIR
Mandatory: no
The total number of reflections phased in the native data set.
Alias: _phasing_MIR.ebi_reflns (ebi_extensions, 1.0)
Type: int
Range: [0, .] [0, 0]
Category: phasing_MIR
Mandatory: no
The number of acentric reflections phased in the native data set.
Alias: _phasing_MIR.ebi_reflns_acentric (ebi_extensions, 1.0)
Type: int
Range: [0, .] [0, 0]
Category: phasing_MIR
Mandatory: no
The number of centric reflections phased in the native data set.
Alias: _phasing_MIR.ebi_reflns_centric (ebi_extensions, 1.0)
Type: int
Range: [0, .] [0, 0]
Category: phasing_MIR
Mandatory: no
Criterion used to limit the reflections used in the phasing calculations.
Alias: _phasing_MIR.ebi_reflns_criteria (ebi_extensions, 1.0)
Type: text
Example:
> 4 \s(I)
Data items in the PHASING_MIR_DER category record details about individual derivatives used in the phasing of the structure when methods involving isomorphous replacement are involved. A derivative in this context does not necessarily equate with a data set; for instance, the same data set could be used to one resolution limit as an isomorphous scatterer and to a different resolution (and with a different sigma cutoff) as an anomalous scatterer. These would be treated as two distinct derivatives, although both derivatives would point to the same data sets via _phasing_MIR_der.der_set_id and _phasing_MIR_der.native_set_id.
Mandatory: no
Keys: _phasing_MIR_der.id
Groups: inclusive_group phasing_group
Examples:
| Example | Detail |
|---|---|
loop_
_phasing_MIR_der.id
_phasing_MIR_der.number_of_sites
_phasing_MIR_der.details
KAu(CN)2 3
'major site interpreted in difference Patterson'
K2HgI4 6 'sites found in cross-difference Fourier'
K3IrCl6 2 'sites found in cross-difference Fourier'
All 11 'data for all three derivatives combined'
|
Example 1 - based on a paper by Zanotti et al. [J. Biol. Chem. (1993), 268, 10728-10738]. |
Category: phasing_MIR_der
Mandatory: yes
The lowest value for the interplanar spacings for the reflection data used for this derivative. This is called the highest resolution.
Type: float
Units: angstroms
Range: [0.0, .] [0.0, 0.0]
Category: phasing_MIR_der
Mandatory: yes
The highest value for the interplanar spacings for the reflection data used for this derivative. This is called the lowest resolution.
Type: float
Units: angstroms
Range: [0.0, .] [0.0, 0.0]
Mandatory: yes
The data set that was treated as the derivative in this experiment. This data item is a pointer to _phasing_set.id in the PHASING_SET category.
Category: phasing_MIR_der
Mandatory: no
A description of special aspects of this derivative, its data, its solution or its use in phasing.
Type: text
| Name | Category | Mandatory |
|---|---|---|
| _phasing_MIR_der.id | phasing_MIR_der | yes |
| _phasing_MIR_der_refln.der_id | phasing_MIR_der_refln | yes |
| _phasing_MIR_der_shell.der_id | phasing_MIR_der_shell | yes |
| _phasing_MIR_der_site.der_id | phasing_MIR_der_site | yes |
The value of _phasing_MIR_der.id must uniquely identify a record in the PHASING_MIR_DER list. Note that this item need not be a number; it can be any unique identifier.
Type: line
Child / Parent relations:
| Child | Parent |
|---|---|
| _phasing_MIR_der_refln.der_id | _phasing_MIR_der.id |
| _phasing_MIR_der_shell.der_id | _phasing_MIR_der.id |
| _phasing_MIR_der_site.der_id | _phasing_MIR_der.id |
Examples:
| Example | Detail |
|---|---|
KAu(CN)2 |
|
K2HgI4_anom |
|
K2HgI4_iso |
Mandatory: yes
The data set that was treated as the native in this experiment. This data item is a pointer to _phasing_set.id in the PHASING_SET category.
Category: phasing_MIR_der
Mandatory: no
The number of heavy-atom sites in this derivative.
Type: int
Category: phasing_MIR_der
Mandatory: no
The mean phasing power P for acentric reflections for this derivative. sum|Fhcalc2| P = (----------------------------)1/2 sum|Fphobs - Fphcalc|2 Fphobs = the observed structure-factor amplitude of this derivative Fphcalc = the calculated structure-factor amplitude of this derivative Fhcalc = the calculated structure-factor amplitude from the heavy-atom model sum is taken over the specified reflections
Alias: _phasing_MIR_der.ebi_power_acentric (ebi_extensions, 1.0)
Type: float
Range: [0.0, .] [0.0, 0.0]
Category: phasing_MIR_der
Mandatory: no
The mean phasing power P for centric reflections for this derivative. sum|Fhcalc2| P = (----------------------------)1/2 sum|Fphobs - Fphcalc|2 Fphobs = the observed structure-factor amplitude of the derivative Fphcalc = the calculated structure-factor amplitude of the derivative Fhcalc = the calculated structure-factor amplitude from the heavy-atom model sum is taken over the specified reflections
Alias: _phasing_MIR_der.ebi_power_centric (ebi_extensions, 1.0)
Type: float
Range: [0.0, .] [0.0, 0.0]
Category: phasing_MIR_der
Mandatory: no
Residual factor Rcullis,acen for acentric reflections for this derivative. The Cullis R factor was originally defined only for centric reflections. It is, however, also a useful statistical measure for acentric reflections, which is how it is used in this data item. sum| |Fphobs +/- Fpobs| - Fhcalc | Rcullis,acen = ---------------------------------------- sum|Fphobs - Fpobs| Fpobs = the observed structure-factor amplitude of the native Fphobs = the observed structure-factor amplitude of the derivative Fhcalc = the calculated structure-factor amplitude from the heavy-atom model sum is taken over the specified reflections Ref: Cullis, A. F., Muirhead, H., Perutz, M. F., Rossmann, M. G. & North, A. C. T. (1961). Proc. R. Soc. London Ser. A, 265, 15-38.
Alias: _phasing_MIR_der.ebi_Rcullis_acentric (ebi_extensions, 1.0)
Type: float
Range: [0.0, .] [0.0, 0.0]
Category: phasing_MIR_der
Mandatory: no
Residual factor Rcullis,ano for anomalous reflections for this derivative. The Cullis R factor was originally defined only for centric reflections. It is, however, also a useful statistical measure for anomalous reflections, which is how it is used in this data item. This is tabulated for acentric terms. A value less than 1.0 means there is some contribution to the phasing from the anomalous data. sum |Fph+obsFph-obs - Fh+calc - Fh-calc| Rcullis,ano = ------------------------------------------------ sum|Fph+obs - Fph-obs| Fph+obs = the observed positive Friedel structure-factor amplitude for the derivative Fph-obs = the observed negative Friedel structure-factor amplitude for the derivative Fh+calc = the calculated positive Friedel structure-factor amplitude from the heavy-atom model Fh-calc = the calculated negative Friedel structure-factor amplitude from the heavy-atom model sum is taken over the specified reflections Ref: Cullis, A. F., Muirhead, H., Perutz, M. F., Rossmann, M. G. & North, A. C. T. (1961). Proc. R. Soc. London Ser. A, 265, 15-38.
Alias: _phasing_MIR_der.ebi_Rcullis_anomalous (ebi_extensions, 1.0)
Type: float
Range: [0.0, .] [0.0, 0.0]
Category: phasing_MIR_der
Mandatory: no
Residual factor Rcullis for centric reflections for this derivative. sum| |Fphobs +/- Fpobs| - Fhcalc | Rcullis = ---------------------------------------- sum|Fphobs - Fpobs| Fpobs = the observed structure-factor amplitude of the native Fphobs = the observed structure-factor amplitude of the derivative Fhcalc = the calculated structure-factor amplitude from the heavy-atom model sum is taken over the specified reflections Ref: Cullis, A. F., Muirhead, H., Perutz, M. F., Rossmann, M. G. & North, A. C. T. (1961). Proc. R. Soc. London Ser. A, 265, 15-38.
Alias: _phasing_MIR_der.ebi_Rcullis_centric (ebi_extensions, 1.0)
Type: float
Range: [0.0, .] [0.0, 0.0]
Category: phasing_MIR_der
Mandatory: no
The number of acentric reflections used in phasing for this derivative.
Alias: _phasing_MIR_der.ebi_reflns_acentric (ebi_extensions, 1.0)
Type: int
Range: [0, .] [0, 0]
Category: phasing_MIR_der
Mandatory: no
The number of anomalous reflections used in phasing for this derivative.
Alias: _phasing_MIR_der.ebi_reflns_anomalous (ebi_extensions, 1.0)
Type: int
Range: [0, .] [0, 0]
Category: phasing_MIR_der
Mandatory: no
The number of centric reflections used in phasing for this derivative.
Alias: _phasing_MIR_der.ebi_reflns_centric (ebi_extensions, 1.0)
Type: int
Range: [0, .] [0, 0]
Category: phasing_MIR_der
Mandatory: no
Criteria used to limit the reflections used in the phasing calculations.
Type: text
Example:
> 4 \s(I)
Data items in the PHASING_MIR_DER_REFLN category record details about the calculated structure factors obtained in an MIR phasing experiment. This list may contain information from a number of different derivatives; _phasing_MIR_der_refln.der_id indicates to which derivative a given record corresponds. (A derivative in this context does not necessarily equate with a data set; see the definition of the PHASING_MIR_DER category for a discussion of the meaning of derivative.) It is not necessary for the data items describing the measured value of F to appear in this list, as they will be given in the PHASING_SET_REFLN category. However, these items can also be listed here for completeness.
Mandatory: no
Keys: _phasing_MIR_der_refln.index_h _phasing_MIR_der_refln.index_k _phasing_MIR_der_refln.index_l _phasing_MIR_der_refln.der_id _phasing_MIR_der_refln.set_id
Groups: inclusive_group phasing_group
Examples:
| Example | Detail |
|---|---|
_phasing_MIR_der_refln.index_h 6
_phasing_MIR_der_refln.index_k 1
_phasing_MIR_der_refln.index_l 25
_phasing_MIR_der_refln.der_id HGPT1
_phasing_MIR_der_refln.set_id 'NS1-96'
_phasing_MIR_der_refln.F_calc_au 106.66
_phasing_MIR_der_refln.F_meas_au 204.67
_phasing_MIR_der_refln.F_meas_sigma 6.21
_phasing_MIR_der_refln.HL_A_iso -3.15
_phasing_MIR_der_refln.HL_B_iso -0.76
_phasing_MIR_der_refln.HL_C_iso 0.65
_phasing_MIR_der_refln.HL_D_iso 0.23
_phasing_MIR_der_refln.phase_calc 194.48
|
Example 1 - based on laboratory records for the 6,1,25 reflection of an Hg/Pt derivative of protein NS1. |
Mandatory: yes
This data item is a pointer to _phasing_MIR_der.id in the PHASING_MIR_DER category.
Category: phasing_MIR_der_refln
Mandatory: no
The calculated value of the structure factor for this derivative, in electrons.
Type: float
Units: electrons
Related item: _phasing_MIR_der_refln.F_calc_au (conversion_arbitrary)
Category: phasing_MIR_der_refln
Mandatory: no
The calculated value of the structure factor for this derivative, in arbitrary units.
Type: float
Units: arbitrary
Related item: _phasing_MIR_der_refln.F_calc (conversion_arbitrary)
Category: phasing_MIR_der_refln
Mandatory: no
The measured value of the structure factor for this derivative, in electrons.
Type: float
Type conditions: esd
Units: electrons
Related items: _phasing_MIR_der_refln.F_meas_sigma (associated_esd) _phasing_MIR_der_refln.F_meas_au (conversion_arbitrary)
Category: phasing_MIR_der_refln
Mandatory: no
The measured value of the structure factor for this derivative, in arbitrary units.
Type: float
Type conditions: esd
Units: arbitrary
Related items: _phasing_MIR_der_refln.F_meas_sigma_au (associated_esd) _phasing_MIR_der_refln.F_meas (conversion_arbitrary)
Category: phasing_MIR_der_refln
Mandatory: no
The standard uncertainty (estimated standard deviation) of _phasing_MIR_der_refln.F_meas, in electrons.
Type: float
Units: electrons
Related items: _phasing_MIR_der_refln.F_meas (associated_value) _phasing_MIR_der_refln.F_meas_sigma_au (conversion_arbitrary)
Category: phasing_MIR_der_refln
Mandatory: no
The standard uncertainty (estimated standard deviation) of _phasing_MIR_der_refln.F_meas_au, in arbitrary units.
Type: float
Units: arbitrary
Related items: _phasing_MIR_der_refln.F_meas_au (associated_value) _phasing_MIR_der_refln.F_meas_sigma (conversion_arbitrary)
Category: phasing_MIR_der_refln
Mandatory: no
The isomorphous Hendrickson-Lattman coefficient Aiso for this reflection for this derivative. -2.0 * (Fpobs2 + Fhcalc2 - Fphobs2) * Fpobs * cos(alphahcalc) Aiso = ----------------------------------------------- E2 E = (Fphobs - Fpobs - Fhcalc)2 for centric reflections = [(Fphobs - Fpobs) * 21/2 - Fhcalc]2 for acentric reflections Fpobs = the observed structure-factor amplitude of the native Fphobs = the observed structure-factor amplitude of the derivative Fhcalc = the calculated structure-factor amplitude from the heavy-atom model alphahcalc = the calculated phase from the heavy-atom model This coefficient appears in the expression for the phase probability of each isomorphous derivative: Pi(alpha) = exp[k + A * cos(alpha) + B * sin(alpha) + C * cos(2 * alpha) + D * sin(2 * alpha)] Ref: Hendrickson, W. A. & Lattman, E. E. (1970). Acta Cryst. B26, 136-143.
Type: float
Category: phasing_MIR_der_refln
Mandatory: no
The isomorphous Hendrickson-Lattman coefficient Biso for this reflection for this derivative. -2.0 * (Fpobs2 + Fhcalc2 - Fphobs2) * Fpobs * sin(alphahcalc) Biso = ----------------------------------------------- E2 E = (Fphobs - Fpobs - Fhcalc)2 for centric reflections = [(Fphobs - Fpobs) * 21/2 - Fhcalc]2 for acentric reflections Fpobs = the observed structure-factor amplitude of the native Fphobs = the observed structure-factor amplitude of the derivative Fhcalc = the calculated structure-factor amplitude from the heavy-atom model alphahcalc = the phase calculated from the heavy-atom model This coefficient appears in the expression for the phase probability of each isomorphous derivative: Pi(alpha) = exp[k + A * cos(alpha) + B * sin(alpha) + C * cos(2 * alpha) + D * sin(2 * alpha)] Ref: Hendrickson, W. A. & Lattman, E. E. (1970). Acta Cryst. B26, 136-143.
Type: float
Category: phasing_MIR_der_refln
Mandatory: no
The isomorphous Hendrickson-Lattman coefficient Ciso for this reflection for this derivative. -Fpobs2 * [sin(alphahcalc)2 - cos(alphahcalc)2] Ciso = ------------------------------------ E2 E = (Fphobs - Fpobs - Fhcalc)2 for centric reflections = [(Fphobs - Fpobs) * 21/2 - Fhcalc]2 for acentric reflections Fpobs = the observed structure-factor amplitude of the native Fphobs = the observed structure-factor amplitude of the derivative Fhcalc = the calculated structure-factor amplitude from the heavy-atom model alphahcalc = the phase calculated from the heavy-atom model This coefficient appears in the expression for the phase probability of each isomorphous derivative: Pi(alpha) = exp[k + A * cos(alpha) + B * sin(alpha) + C * cos(2 * alpha) + D * sin(2 * alpha)] Ref: Hendrickson, W. A. & Lattman, E. E. (1970). Acta Cryst. B26, 136-143.
Type: float
Category: phasing_MIR_der_refln
Mandatory: no
The isomorphous Hendrickson-Lattman coefficient Diso for this reflection for this derivative. -2.0 * Fpobs2 * sin(alphahcalc)2 * cos(alphahcalc)2 Diso = ---------------------------------------- E2 E = (Fphobs - Fpobs - Fhcalc)2 for centric reflections = [(Fphobs - Fpobs) * 21/2 - Fhcalc]2 for acentric reflections Fpobs = the observed structure-factor amplitude of the native Fphobs = the observed structure-factor amplitude of the derivative Fhcalc = the calculated structure-factor amplitude from the heavy-atom model alphahcalc = the phase calculated from the heavy-atom model This coefficient appears in the expression for the phase probability of each isomorphous derivative: Pi(alpha) = exp[k + A * cos(alpha) + B * sin(alpha) + C * cos(2 * alpha) + D * sin(2 * alpha)] Ref: Hendrickson, W. A. & Lattman, E. E. (1970). Acta Cryst. B26, 136-143.
Type: float
Category: phasing_MIR_der_refln
Mandatory: yes
Sub-category: miller_index
Miller index h for this reflection for this derivative.
Type: int
Dependent items: _phasing_MIR_der_refln.index_k _phasing_MIR_der_refln.index_l
Category: phasing_MIR_der_refln
Mandatory: yes
Sub-category: miller_index
Miller index k for this reflection for this derivative.
Type: int
Dependent items: _phasing_MIR_der_refln.index_h _phasing_MIR_der_refln.index_l
Category: phasing_MIR_der_refln
Mandatory: yes
Sub-category: miller_index
Miller index l for this reflection for this derivative.
Type: int
Dependent items: _phasing_MIR_der_refln.index_h _phasing_MIR_der_refln.index_k
Category: phasing_MIR_der_refln
Mandatory: no
The calculated value of the structure-factor phase based on the heavy-atom model for this derivative in degrees.
Type: float
Units: degrees
Mandatory: yes
This data item is a pointer to _phasing_set.id in the PHASING_SET category.
Data items in the PHASING_MIR_DER_SHELL category record statistics, broken down into shells of resolution, for an MIR phasing experiment. This list may contain information from a number of different derivatives; _phasing_MIR_der_shell.der_id indicates to which derivative a given record corresponds. (A derivative in this context does not necessarily equate with a data set; see the definition of the PHASING_MIR_DER category for a discussion of the meaning of derivative.)
Mandatory: no
Keys: _phasing_MIR_der_shell.der_id _phasing_MIR_der_shell.d_res_low _phasing_MIR_der_shell.d_res_high
Groups: inclusive_group phasing_group
Examples:
| Example | Detail |
|---|---|
loop_
_phasing_MIR_der_shell.der_id
_phasing_MIR_der_shell.d_res_low
_phasing_MIR_der_shell.d_res_high
_phasing_MIR_der_shell.ha_ampl
_phasing_MIR_der_shell.loc
KAu(CN)2 15.0 8.3 54 26
KAu(CN)2 8.3 6.4 54 20
KAu(CN)2 6.4 5.2 50 20
KAu(CN)2 5.2 4.4 44 23
KAu(CN)2 4.4 3.8 39 23
KAu(CN)2 3.8 3.4 33 21
KAu(CN)2 3.4 3.0 28 17
KAu(CN)2 15.0 3.0 38 21
K2HgI4 15.0 8.3 149 87
K2HgI4 8.3 6.4 121 73
K2HgI4 6.4 5.2 95 61
K2HgI4 5.2 4.4 80 60
K2HgI4 4.4 3.8 73 63
K2HgI4 3.8 3.4 68 57
K2HgI4 3.4 3.0 63 46
K2HgI4 15.0 3.0 79 58
K3IrCl6 15.0 8.3 33 27
K3IrCl6 8.3 6.4 40 23
K3IrCl6 6.4 5.2 31 22
K3IrCl6 5.2 4.4 27 23
K3IrCl6 4.4 3.8 22 23
K3IrCl6 3.8 3.4 19 20
K3IrCl6 3.4 3.0 16 20
K3IrCl6 15.0 3.0 23 21
|
Example 1 - based on a paper by Zanotti et al. [J. Biol. Chem. (1993), 268, 10728-10738] with addition of an arbitrary low-resolution limit. |
Category: phasing_MIR_der_shell
Mandatory: yes
The lowest value for the interplanar spacings for the reflection data for this derivative in this shell. This is called the highest resolution.
Type: float
Units: angstroms
Range: [0.0, .] [0.0, 0.0]
Category: phasing_MIR_der_shell
Mandatory: yes
The highest value for the interplanar spacings for the reflection data for this derivative in this shell. This is called the lowest resolution.
Type: float
Units: angstroms
Range: [0.0, .] [0.0, 0.0]
Mandatory: yes
This data item is a pointer to _phasing_MIR_der.id in the PHASING_MIR_DER category.
Category: phasing_MIR_der_shell
Mandatory: no
The mean value of the figure of merit m for reflections for this derivative in this shell. int Palpha exp(i*alpha) dalpha m = -------------------------------- int Palpha dalpha Palpha = the probability that the phase angle alpha is correct int is taken over the range alpha = 0 to 2 pi.
Type: float
Range: [0.0, .] [0.0, 0.0]
Category: phasing_MIR_der_shell
Mandatory: no
The mean heavy-atom amplitude for reflections for this derivative in this shell.
Type: float
Range: [0.0, .] [0.0, 0.0]
Category: phasing_MIR_der_shell
Mandatory: no
The mean lack-of-closure error loc for reflections for this derivative in this shell. loc = sum|Fphobs - Fphcalc| Fphobs = the observed structure-factor amplitude of the derivative Fphcalc = the calculated structure-factor amplitude of the derivative sum is taken over the specified reflections
Type: float
Range: [0.0, .] [0.0, 0.0]
Category: phasing_MIR_der_shell
Mandatory: no
The mean of the phase values for reflections for this derivative in this shell.
Type: float
Category: phasing_MIR_der_shell
Mandatory: no
The mean phasing power P for reflections for this derivative in this shell. sum|Fhcalc2| P = (----------------------------)1/2 sum|Fphobs - Fphcalc|2 Fphobs = the observed structure-factor amplitude of the derivative Fphcalc = the calculated structure-factor amplitude of the derivative Fhcalc = the calculated structure-factor amplitude from the heavy-atom model sum is taken over the specified reflections
Type: float
Range: [0.0, .] [0.0, 0.0]
Category: phasing_MIR_der_shell
Mandatory: no
Residual factor Rcullis for centric reflections for this derivative in this shell. sum| |Fphobs +/- Fpobs| - Fhcalc | Rcullis = ---------------------------------------- sum|Fphobs - Fpobs| Fpobs = the observed structure-factor amplitude of the native Fphobs = the observed structure-factor amplitude of the derivative Fhcalc = the calculated structure-factor amplitude from the heavy-atom model sum is taken over the specified reflections Ref: Cullis, A. F., Muirhead, H., Perutz, M. F., Rossmann, M. G. & North, A. C. T. (1961). Proc. R. Soc. London Ser. A, 265, 15-38.
Type: float
Range: [0.0, .] [0.0, 0.0]
Category: phasing_MIR_der_shell
Mandatory: no
Residual factor Rkraut for general reflections for this derivative in this shell. sum|Fphobs - Fphcalc| Rkraut = ------------------------- sum|Fphobs| Fphobs = the observed structure-factor amplitude of the derivative Fphcalc = the calculated structure-factor amplitude of the derivative sum is taken over the specified reflections Ref: Kraut, J., Sieker, L. C., High, D. F. & Freer, S. T. (1962). Proc. Natl Acad. Sci. USA, 48, 1417-1424.
Type: float
Range: [0.0, .] [0.0, 0.0]
Category: phasing_MIR_der_shell
Mandatory: no
The number of reflections in this shell.
Type: int
Range: [0, .] [0, 0]
Data items in the PHASING_MIR_DER_SITE category record details about the heavy-atom sites in an MIR phasing experiment. This list may contain information from a number of different derivatives; _phasing_MIR_der_site.der_id indicates to which derivative a given record corresponds. (A derivative in this context does not necessarily equate with a data set; see the definition of the PHASING_MIR_DER category for a discussion of the meaning of derivative.)
Mandatory: no
Keys: _phasing_MIR_der_site.der_id _phasing_MIR_der_site.id
Groups: inclusive_group phasing_group
Examples:
| Example | Detail |
|---|---|
loop_
_phasing_MIR_der_site.der_id
_phasing_MIR_der_site.id
_phasing_MIR_der_site.atom_type_symbol
_phasing_MIR_der_site.occupancy
_phasing_MIR_der_site.fract_x
_phasing_MIR_der_site.fract_y
_phasing_MIR_der_site.fract_z
_phasing_MIR_der_site.B_iso
KAu(CN)2 1 Au 0.40 0.082 0.266 0.615 33.0
KAu(CN)2 2 Au 0.03 0.607 0.217 0.816 25.9
KAu(CN)2 3 Au 0.02 0.263 0.782 0.906 15.7
K2HgI4 1 Hg 0.63 0.048 0.286 0.636 33.7
K2HgI4 2 Hg 0.34 0.913 0.768 0.889 36.7
K2HgI4 3 Hg 0.23 0.974 0.455 0.974 24.2
K2HgI4 4 Hg 0.28 0.903 0.836 0.859 14.7
K2HgI4 5 Hg 0.07 0.489 0.200 0.885 6.4
K2HgI4 6 Hg 0.07 0.162 0.799 0.889 32.9
K3IrCl6 1 Ir 0.26 0.209 0.739 0.758 40.8
K3IrCl6 2 Ir 0.05 0.279 0.613 0.752 24.9
|
Example 1 - based on a paper by Zanotti et al. [J. Biol. Chem. (1993), 268, 10728-10738] with occupancies converted from electrons to fractional. |
Mandatory: yes
This data item is a pointer to _atom_type.symbol in the ATOM_TYPE category. The scattering factors referenced via this data item should be those used in the refinement of the heavy-atom data; in some cases this is the scattering factor for the single heavy atom, in other cases these are the scattering factors for an atomic cluster.
Category: phasing_MIR_der_site
Mandatory: no
Isotropic displacement parameter for this heavy-atom site in this derivative.
Type: float
Type conditions: esd
Units: angstroms
Related item: _phasing_MIR_der_site.B_iso_esd (associated_esd)
Category: phasing_MIR_der_site
Mandatory: no
The standard uncertainty (estimated standard deviation) of _phasing_MIR_der_site.B_iso.
Type: float
Units: angstroms
Related item: _phasing_MIR_der_site.B_iso (associated_value)
Category: phasing_MIR_der_site
Mandatory: no
Sub-category: cartesian_coordinate
The x coordinate of this heavy-atom position in this derivative specified as orthogonal angstroms. The orthogonal Cartesian axes are related to the cell axes as specified by the description given in _atom_sites.Cartn_transform_axes.
Type: float
Type conditions: esd
Units: angstroms
Dependent items: _phasing_MIR_der_site.Cartn_y _phasing_MIR_der_site.Cartn_z
Related item: _phasing_MIR_der_site.Cartn_x_esd (associated_esd)
Category: phasing_MIR_der_site
Mandatory: no
Sub-category: cartesian_coordinate_esd
The standard uncertainty (estimated standard deviation) of _phasing_MIR_der_site.Cartn_x.
Type: float
Units: angstroms
Dependent items: _phasing_MIR_der_site.Cartn_y_esd _phasing_MIR_der_site.Cartn_z_esd
Related item: _phasing_MIR_der_site.Cartn_x (associated_value)
Category: phasing_MIR_der_site
Mandatory: no
Sub-category: cartesian_coordinate
The y coordinate of this heavy-atom position in this derivative specified as orthogonal angstroms. The orthogonal Cartesian axes are related to the cell axes as specified by the description given in _atom_sites.Cartn_transform_axes.
Type: float
Type conditions: esd
Units: angstroms
Dependent items: _phasing_MIR_der_site.Cartn_x _phasing_MIR_der_site.Cartn_z
Related item: _phasing_MIR_der_site.Cartn_y_esd (associated_esd)
Category: phasing_MIR_der_site
Mandatory: no
Sub-category: cartesian_coordinate_esd
The standard uncertainty (estimated standard deviation) of _phasing_MIR_der_site.Cartn_y.
Type: float
Units: angstroms
Dependent items: _phasing_MIR_der_site.Cartn_x_esd _phasing_MIR_der_site.Cartn_z_esd
Related item: _phasing_MIR_der_site.Cartn_y (associated_value)
Category: phasing_MIR_der_site
Mandatory: no
Sub-category: cartesian_coordinate
The z coordinate of this heavy-atom position in this derivative specified as orthogonal angstroms. The orthogonal Cartesian axes are related to the cell axes as specified by the description given in _atom_sites.Cartn_transform_axes.
Type: float
Type conditions: esd
Units: angstroms
Dependent items: _phasing_MIR_der_site.Cartn_x _phasing_MIR_der_site.Cartn_y
Related item: _phasing_MIR_der_site.Cartn_z_esd (associated_esd)
Category: phasing_MIR_der_site
Mandatory: no
Sub-category: cartesian_coordinate_esd
The standard uncertainty (estimated standard deviation) of _phasing_MIR_der_site.Cartn_z.
Type: float
Units: angstroms
Dependent items: _phasing_MIR_der_site.Cartn_x_esd _phasing_MIR_der_site.Cartn_y_esd
Related item: _phasing_MIR_der_site.Cartn_z (associated_value)
Mandatory: yes
This data item is a pointer to _phasing_MIR_der.id in the PHASING_MIR_DER category.
Category: phasing_MIR_der_site
Mandatory: no
A description of special aspects of the derivative site.
Type: text
Examples:
| Example | Detail |
|---|---|
binds to His 117 |
|
minor site obtained from difference Fourier |
|
same as site 2 in the K2HgI4 derivative |
Category: phasing_MIR_der_site
Mandatory: no
Sub-category: fractional_coordinate
The x coordinate of this heavy-atom position in this derivative specified as a fraction of _cell.length_a.
Type: float
Type conditions: esd
Dependent items: _phasing_MIR_der_site.fract_y _phasing_MIR_der_site.fract_z
Related item: _phasing_MIR_der_site.fract_x_esd (associated_esd)
Category: phasing_MIR_der_site
Mandatory: no
Sub-category: fractional_coordinate_esd
The standard uncertainty (estimated standard deviation) of _phasing_MIR_der_site.fract_x.
Type: float
Dependent items: _phasing_MIR_der_site.fract_y_esd _phasing_MIR_der_site.fract_z_esd
Related item: _phasing_MIR_der_site.fract_x (associated_value)
Category: phasing_MIR_der_site
Mandatory: no
Sub-category: fractional_coordinate
The y coordinate of this heavy-atom position in this derivative specified as a fraction of _cell.length_b.
Type: float
Type conditions: esd
Dependent items: _phasing_MIR_der_site.fract_x _phasing_MIR_der_site.fract_z
Related item: _phasing_MIR_der_site.fract_y_esd (associated_esd)
Category: phasing_MIR_der_site
Mandatory: no
Sub-category: fractional_coordinate_esd
The standard uncertainty (estimated standard deviation) of _phasing_MIR_der_site.fract_y.
Type: float
Dependent items: _phasing_MIR_der_site.fract_x_esd _phasing_MIR_der_site.fract_z_esd
Related item: _phasing_MIR_der_site.fract_y (associated_value)
Category: phasing_MIR_der_site
Mandatory: no
Sub-category: fractional_coordinate
The z coordinate of this heavy-atom position in this derivative specified as a fraction of _cell.length_c.
Type: float
Type conditions: esd
Dependent items: _phasing_MIR_der_site.fract_x _phasing_MIR_der_site.fract_y
Related item: _phasing_MIR_der_site.fract_z_esd (associated_esd)
Category: phasing_MIR_der_site
Mandatory: no
Sub-category: fractional_coordinate_esd
The standard uncertainty (estimated standard deviation) of _phasing_MIR_der_site.fract_z.
Type: float
Dependent items: _phasing_MIR_der_site.fract_x_esd _phasing_MIR_der_site.fract_y_esd
Related item: _phasing_MIR_der_site.fract_z (associated_value)
Category: phasing_MIR_der_site
Mandatory: yes
The value of _phasing_MIR_der_site.id must uniquely identify each site in each derivative in the PHASING_MIR_DER_SITE list. The atom identifiers need not be unique over all sites in all derivatives; they need only be unique for each site in each derivative. Note that this item need not be a number; it can be any unique identifier.
Type: code
Category: phasing_MIR_der_site
Mandatory: no
The fraction of the atom type present at this heavy-atom site in a given derivative. The sum of the occupancies of all the atom types at this site may not significantly exceed 1.0 unless it is a dummy site.
Type: float
Default value: 1.0
Range: [0.0, .] [0.0, 0.0]
Category: phasing_MIR_der_site
Mandatory: no
The relative anomalous occupancy of the atom type present at this heavy-atom site in a given derivative. This atom occupancy will probably be on an arbitrary scale.
Alias: _phasing_MIR_der_site.ebi_occupancy_anom (ebi_extensions, 1.0)
Type: float
Type conditions: esd
Related item: _phasing_MIR_der_site.occupancy_anom_su (associated_esd)
Category: phasing_MIR_der_site
Mandatory: no
The standard uncertainty (estimated standard deviation) of _phasing_MIR_der_site.occupancy_anom.
Alias: _phasing_MIR_der_site.ebi_occupancy_anom_esd (ebi_extensions, 1.0)
Type: float
Related item: _phasing_MIR_der_site.occupancy_anom (associated_value)
Category: phasing_MIR_der_site
Mandatory: no
The relative real isotropic occupancy of the atom type present at this heavy-atom site in a given derivative. This atom occupancy will probably be on an arbitrary scale.
Alias: _phasing_MIR_der_site.ebi_occupancy_iso (ebi_extensions, 1.0)
Type: float
Type conditions: esd
Related item: _phasing_MIR_der_site.occupancy_iso_su (associated_esd)
Category: phasing_MIR_der_site
Mandatory: no
The standard uncertainty (estimated standard deviation) of _phasing_MIR_der_site.occupancy_iso.
Alias: _phasing_MIR_der_site.ebi_occupancy_iso_esd (ebi_extensions, 1.0)
Type: float
Related item: _phasing_MIR_der_site.occupancy_iso (associated_value)
Data items in the PHASING_MIR_SHELL category record statistics for an isomorphous replacement phasing experiment.broken down into shells of resolution.
Mandatory: no
Keys: _phasing_MIR_shell.d_res_low _phasing_MIR_shell.d_res_high
Groups: inclusive_group phasing_group
Examples:
| Example | Detail |
|---|---|
loop_
_phasing_MIR_shell.d_res_low
_phasing_MIR_shell.d_res_high
_phasing_MIR_shell.reflns
_phasing_MIR_shell.FOM
15.0 8.3 80 0.69
8.3 6.4 184 0.73
6.4 5.2 288 0.72
5.2 4.4 406 0.65
4.4 3.8 554 0.54
3.8 3.4 730 0.53
3.4 3.0 939 0.50
|
Example 1 - based on a paper by Zanotti et al. [J. Biol. Chem. (1993), 268, 10728-10738] with addition of an arbitrary low-resolution limit. |
Category: phasing_MIR_shell
Mandatory: yes
The lowest value for the interplanar spacings for the reflection data in this shell. This is called the highest resolution. Note that the resolution limits of shells in the items _phasing_MIR_shell.d_res_high and _phasing_MIR_shell.d_res_low are independent of the resolution limits of shells in the items _reflns_shell.d_res_high and _reflns_shell.d_res_low.
Type: float
Units: angstroms
Range: [0.0, .] [0.0, 0.0]
Category: phasing_MIR_shell
Mandatory: yes
The highest value for the interplanar spacings for the reflection data in this shell. This is called the lowest resolution. Note that the resolution limits of shells in the items _phasing_MIR_shell.d_res_high and _phasing_MIR_shell.d_res_low are independent of the resolution limits of shells in the items _reflns_shell.d_res_high and _reflns_shell.d_res_low.
Type: float
Units: angstroms
Range: [0.0, .] [0.0, 0.0]
Category: phasing_MIR_shell
Mandatory: no
The mean value of the figure of merit m for reflections in this shell. int Palpha exp(i*alpha) dalpha m = -------------------------------- int Palpha dalpha Palpha = the probability that the phase angle alpha is correct the integral is taken over the range alpha = 0 to 2 pi.
Type: float
Range: [0.0, .] [0.0, 0.0]
Category: phasing_MIR_shell
Mandatory: no
The mean value of the figure of merit m for acentric reflections in this shell. int Palpha exp(i*alpha) dalpha m = -------------------------------- int Palpha dalpha Pa = the probability that the phase angle a is correct the integral is taken over the range alpha = 0 to 2 pi.
Alias: _phasing_MIR_shell.ebi_fom_acentric (ebi_extensions, 1.0)
Type: float
Range: [0.0, .] [0.0, 0.0]
Category: phasing_MIR_shell
Mandatory: no
The mean value of the figure of merit m for centric reflections in this shell. int Palpha exp(i*alpha) dalpha m = -------------------------------- int Palpha dalpha Pa = the probability that the phase angle a is correct the integral is taken over the range alpha = 0 to 2 pi.
Alias: _phasing_MIR_shell.ebi_fom_centric (ebi_extensions, 1.0)
Type: float
Range: [0.0, .] [0.0, 0.0]
Category: phasing_MIR_shell
Mandatory: no
The mean lack-of-closure error loc for reflections in this shell. loc = sum|Fphobs - Fphcalc| Fphobs = the observed structure-factor amplitude of the derivative Fphcalc = the calculated structure-factor amplitude of the derivative sum is taken over the specified reflections
Type: float
Range: [0.0, .] [0.0, 0.0]
Category: phasing_MIR_shell
Mandatory: no
The mean of the phase values for all reflections in this shell.
Type: float
Category: phasing_MIR_shell
Mandatory: no
The mean phasing power P for reflections in this shell. sum|Fhcalc2| P = (----------------------------)1/2 sum|Fphobs - Fphcalc|2 Fphobs = the observed structure-factor amplitude of the derivative Fphcalc = the calculated structure-factor amplitude of the derivative Fhcalc = the calculated structure-factor amplitude from the heavy-atom model sum is taken over the specified reflections
Type: float
Range: [0.0, .] [0.0, 0.0]
Category: phasing_MIR_shell
Mandatory: no
Residual factor Rcullis for centric reflections in this shell. sum| |Fphobs +/- Fpobs| - Fhcalc | Rcullis = ---------------------------------------- sum|Fphobs - Fpobs| Fpobs = the observed structure-factor amplitude of the native Fphobs = the observed structure-factor amplitude of the derivative Fhcalc = the calculated structure-factor amplitude from the heavy-atom model sum is taken over the specified reflections Ref: Cullis, A. F., Muirhead, H., Perutz, M. F., Rossmann, M. G. & North, A. C. T. (1961). Proc. R. Soc. London Ser. A, 265, 15-38.
Type: float
Range: [0.0, .] [0.0, 0.0]
Category: phasing_MIR_shell
Mandatory: no
Residual factor Rkraut for general reflections in this shell. sum|Fphobs - Fphcalc| Rkraut = ------------------------- sum|Fphobs| Fphobs = the observed structure-factor amplitude of the derivative Fphcalc = the calculated structure-factor amplitude of the derivative sum is taken over the specified reflections Ref: Kraut, J., Sieker, L. C., High, D. F. & Freer, S. T. (1962). Proc. Natl Acad. Sci. USA, 48, 1417-1424.
Type: float
Range: [0.0, .] [0.0, 0.0]
Category: phasing_MIR_shell
Mandatory: no
The number of reflections in this shell.
Type: int
Range: [0, .] [0, 0]
Category: phasing_MIR_shell
Mandatory: no
The number of acentric reflections in this shell.
Alias: _phasing_MIR_shell.ebi_reflns_acentric (ebi_extensions, 1.0)
Type: int
Range: [0, .] [0, 0]
Category: phasing_MIR_shell
Mandatory: no
The number of anomalous reflections in this shell.
Type: int
Range: [0, .] [0, 0]
Category: phasing_MIR_shell
Mandatory: no
The number of centric reflections in this shell.
Alias: _phasing_MIR_shell.ebi_reflns_centric (ebi_extensions, 1.0)
Type: int
Range: [0, .] [0, 0]
Data items in the PHASING_SET category record details about the data sets used in a phasing experiment. A given data set may be used in a number of different ways; for instance, a single data set could be used both as an isomorphous derivative and as a component of a multiple-wavelength calculation. This category establishes identifiers for each data set and permits the archiving of a subset of experimental information for each data set (cell constants, wavelength, temperature etc.). This and related categories of data items are provided so that derivative intensity and phase information can be stored in the same data block as the information for the refined structure. If all the possible experimental information for each data set (raw data sets, crystal growth conditions etc.) is to be archived, these data items should be recorded in a separate data block.
Mandatory: no
Keys: _phasing_set.id
Groups: inclusive_group phasing_group
Examples:
| Example | Detail |
|---|---|
_phasing_set.id 'NS1-96'
_phasing_set.cell_angle_alpha 90.0
_phasing_set.cell_angle_beta 90.0
_phasing_set.cell_angle_gamma 90.0
_phasing_set.cell_length_a 38.63
_phasing_set.cell_length_b 38.63
_phasing_set.cell_length_c 82.88
_phasing_set.radiation_wavelength 1.5145
_phasing_set.detector_type 'image plate'
_phasing_set.detector_specific 'RXII'
|
Example 1 - based on laboratory records for an Hg/Pt derivative of protein NS1. |
Category: phasing_set
Mandatory: no
Sub-category: cell_angle
Unit-cell angle alpha for this data set in degrees.
Type: float
Units: degrees
Dependent items: _phasing_set.cell_angle_beta _phasing_set.cell_angle_gamma
Default value: 90.0
Range: [180.0, 180.0] [0.0, 180.0] [0.0, 0.0]
Category: phasing_set
Mandatory: no
Sub-category: cell_angle
Unit-cell angle beta for this data set in degrees.
Type: float
Units: degrees
Dependent items: _phasing_set.cell_angle_alpha _phasing_set.cell_angle_gamma
Default value: 90.0
Range: [180.0, 180.0] [0.0, 180.0] [0.0, 0.0]
Category: phasing_set
Mandatory: no
Sub-category: cell_angle
Unit-cell angle gamma for this data set in degrees.
Type: float
Units: degrees
Dependent items: _phasing_set.cell_angle_alpha _phasing_set.cell_angle_beta
Default value: 90.0
Range: [180.0, 180.0] [0.0, 180.0] [0.0, 0.0]
Category: phasing_set
Mandatory: no
Sub-category: cell_length
Unit-cell length a for this data set in angstroms.
Type: float
Units: angstroms
Dependent items: _phasing_set.cell_length_b _phasing_set.cell_length_c
Range: [0.0, .] [0.0, 0.0]
Category: phasing_set
Mandatory: no
Sub-category: cell_length
Unit-cell length b for this data set in angstroms.
Type: float
Units: angstroms
Dependent items: _phasing_set.cell_length_a _phasing_set.cell_length_c
Range: [0.0, .] [0.0, 0.0]
Category: phasing_set
Mandatory: no
Sub-category: cell_length
Unit-cell length c for this data set in angstroms.
Type: float
Units: angstroms
Dependent items: _phasing_set.cell_length_a _phasing_set.cell_length_b
Range: [0.0, .] [0.0, 0.0]
Category: phasing_set
Mandatory: no
The particular radiation detector. In general, this will be a manufacturer, description, model number or some combination of these.
Type: text
Examples:
| Example | Detail |
|---|---|
Siemens model x |
|
Kodak XG |
|
MAR Research model y |
Category: phasing_set
Mandatory: no
The general class of the radiation detector.
Type: text
Examples:
| Example | Detail |
|---|---|
multiwire |
|
imaging plate |
|
CCD |
|
film |
| Name | Category | Mandatory |
|---|---|---|
| _phasing_set.id | phasing_set | yes |
| _phasing_set_refln.set_id | phasing_set_refln | yes |
| _phasing_MAD_set.set_id | phasing_MAD_set | yes |
| _phasing_MIR_der.der_set_id | phasing_MIR_der | yes |
| _phasing_MIR_der.native_set_id | phasing_MIR_der | yes |
| _phasing_MIR_der_refln.set_id | phasing_MIR_der_refln | yes |
The value of _phasing_set.id must uniquely identify a record in the PHASING_SET list. Note that this item need not be a number; it can be any unique identifier.
Type: line
Child / Parent relations:
Examples:
| Example | Detail |
|---|---|
KAu(CN)2 |
|
K2HgI4 |
Category: phasing_set
Mandatory: no
The particular source of radiation. In general, this will be a manufacturer, description, or model number (or some combination of these) for laboratory sources and an institution name and beamline name for synchrotron sources.
Type: text
Examples:
| Example | Detail |
|---|---|
Rigaku RU200 |
|
Philips fine focus Mo |
|
NSLS beamline X8C |
Category: phasing_set
Mandatory: no
The mean wavelength of the radiation used to measure this data set.
Type: float
Units: angstroms
Range: [0.0, .] [0.0, 0.0]
Category: phasing_set
Mandatory: no
The temperature in kelvins at which the data set was measured.
Type: float
Units: kelvins
Range: [0.0, .] [0.0, 0.0]
Data items in the PHASING_SET_REFLN category record the values of the measured structure factors used in a phasing experiment. This list may contain information from a number of different data sets; _phasing_set_refln.set_id indicates the data set to which a given record corresponds.
Mandatory: no
Keys: _phasing_set_refln.index_h _phasing_set_refln.index_k _phasing_set_refln.index_l _phasing_set_refln.set_id
Groups: inclusive_group phasing_group
Examples:
| Example | Detail |
|---|---|
_phasing_set_refln.set_id 'NS1-96'
_phasing_set_refln.index_h 15
_phasing_set_refln.index_k 15
_phasing_set_refln.index_l 32
_phasing_set_refln.F_meas_au 181.79
_phasing_set_refln.F_meas_sigma_au 3.72
|
Example 1 - based on laboratory records for the 15,15,32 reflection of an Hg/Pt derivative of protein NS1. |
Mandatory: yes
This data item is a pointer to _phasing_set.id in the PHASING_SET category.
Category: phasing_set_refln
Mandatory: no
The measured value of the structure factor for this reflection in this data set in electrons.
Type: float
Type conditions: esd
Units: electrons
Related items: _phasing_set_refln.F_meas_sigma (associated_esd) _phasing_set_refln.F_meas_au (conversion_arbitrary)
Category: phasing_set_refln
Mandatory: no
The measured value of the structure factor for this reflection in this data set in arbitrary units.
Type: float
Type conditions: esd
Units: arbitrary
Related items: _phasing_set_refln.F_meas_sigma_au (associated_esd) _phasing_set_refln.F_meas (conversion_arbitrary)
Category: phasing_set_refln
Mandatory: no
The standard uncertainty (estimated standard deviation) of _phasing_set_refln.F_meas in electrons.
Type: float
Units: electrons
Related items: _phasing_set_refln.F_meas (associated_value) _phasing_set_refln.F_meas_sigma_au (conversion_arbitrary)
Category: phasing_set_refln
Mandatory: no
The standard uncertainty (estimated standard deviation) of _phasing_set_refln.F_meas_au in arbitrary units.
Type: float
Units: arbitrary
Related items: _phasing_set_refln.F_meas_au (associated_value) _phasing_set_refln.F_meas_sigma (conversion_arbitrary)
Category: phasing_set_refln
Mandatory: yes
Sub-category: miller_index
Miller index h of this reflection in this data set.
Type: int
Dependent items: _phasing_set_refln.index_k _phasing_set_refln.index_l
Category: phasing_set_refln
Mandatory: yes
Sub-category: miller_index
Miller index k of this reflection in this data set.
Type: int
Dependent items: _phasing_set_refln.index_h _phasing_set_refln.index_l
Category: phasing_set_refln
Mandatory: yes
Sub-category: miller_index
Miller index l of this reflection in this data set.
Type: int
Dependent items: _phasing_set_refln.index_h _phasing_set_refln.index_k
Data items in the PUBL category are used when submitting a manuscript for publication.
Mandatory: no
Keys: _publ.entry_id
Groups: inclusive_group iucr_group
Examples:
| Example | Detail |
|---|---|
_publ.section_title
; trans-3-Benzoyl-2-(tert-butyl)-4-(iso-butyl)-
1,3-oxazolidin-5-one
;
_publ.section_abstract
; The oxazolidinone ring is a shallow envelope
conformation with the tert-butyl and iso-butyl groups
occupying trans-positions with respect to the ring. The
angles at the N atom sum to 356.2\%, indicating a very
small degree of pyramidalization at this atom. This is
consistent with electron delocalization between the N
atom and the carbonyl centre [N-C=O = 1.374(3)\%A].
;
|
Example 1 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. |
_publ.section_title
; Hemiasterlin methyl ester
;
_publ.section_title_footnote
; IUPAC name: methyl 2,5-dimethyl-4-{2-[3-methyl-
2-methylamino-3-(N-methylbenzo[b]pyrrol-
3-yl)butanamido]-3,3-dimethyl-N-methyl-
butanamido}-2-hexenoate.
;
|
Example 2 - based on C~31~H~48~N~4~O~4~, reported by Coleman, Patrick, Andersen & Rettig [Acta Cryst. (1996), C52, 1525-1527]. |
Mandatory: yes
This data item is a pointer to _entry.id in the ENTRY category.
Category: publ
Mandatory: no
The name and address of the author submitting the manuscript and data block. This is the person contacted by the journal editorial staff. It is preferable to use the separate data items _publ.contact_author_name and _publ.contact_author_address.
Alias: _publ_contact_author (cif_core.dic, 2.0.1)
Type: text
Example:
Professor George Ferguson
Department of Chemistry and Biochemistry
University of Guelph
Ontario
Canada
N1G 2W1
Category: publ
Mandatory: no
The address of the author submitting the manuscript and data block. This is the person contacted by the journal editorial staff.
Alias: _publ_contact_author_address (cif_core.dic, 2.0.1)
Type: text
Example:
Department of Chemistry and Biochemistry
University of Guelph
Ontario
Canada
N1G 2W1
Category: publ
Mandatory: no
E-mail address in a form recognizable to international networks. The format of e-mail addresses is given in Section 3.4, Address Specification, of Internet Message Format, RFC 2822, P. Resnick (Editor), Network Standards Group, April 2001.
Alias: _publ_contact_author_email (cif_core.dic, 2.0.1)
Type: line
Examples:
| Example | Detail |
|---|---|
name@host.domain.country |
|
uur5@banjo.bitnet |
Category: publ
Mandatory: no
Facsimile telephone number of the author submitting the manuscript and data block. The recommended style starts with the international dialing prefix, followed by the area code in parentheses, followed by the local number with no spaces. The earlier convention of including the international dialing prefix in parentheses is no longer recommended.
Alias: _publ_contact_author_fax (cif_core.dic, 2.0.1)
Type: line
Examples:
| Example | Detail |
|---|---|
12(34)9477330 |
|
12()349477330 |
Category: publ
Mandatory: no
The name of the author submitting the manuscript and data block. This is the person contacted by the journal editorial staff.
Alias: _publ_contact_author_name (cif_core.dic, 2.0.1)
Type: text
Example:
Professor George Ferguson
Category: publ
Mandatory: no
Telephone number of the author submitting the manuscript and data block. The recommended style starts with the international dialing prefix, followed by the area code in parentheses, followed by the local number and any extension number prefixed by 'x', with no spaces. The earlier convention of including the international dialing prefix in parentheses is no longer recommended.
Alias: _publ_contact_author_phone (cif_core.dic, 2.0.1)
Type: line
Examples:
| Example | Detail |
|---|---|
12(34)9477330 |
|
12()349477330 |
|
12(34)9477330x5543 |
Category: publ
Mandatory: no
A letter submitted to the journal editor by the contact author.
Alias: _publ_contact_letter (cif_core.dic, 2.0.1)
Type: text
Category: publ
Mandatory: no
A description of the word-processor package and computer used to create the word-processed manuscript stored as _publ.manuscript_processed.
Alias: _publ_manuscript_creation (cif_core.dic, 2.0.1)
Type: text
Example:
Tex file created by FrameMaker on a Sun 3/280
Category: publ
Mandatory: no
The full manuscript of a paper (excluding possibly the figures and the tables) output in ASCII characters from a word processor. Information about the generation of this data item must be specified in the data item _publ.manuscript_creation.
Alias: _publ_manuscript_processed (cif_core.dic, 2.0.1)
Type: text
Category: publ
Mandatory: no
The full manuscript of a paper (excluding figures and possibly the tables) output as standard ASCII text.
Alias: _publ_manuscript_text (cif_core.dic, 2.0.1)
Type: text
Category: publ
Mandatory: no
The category of paper submitted. For submission to Acta Crystallographica Section C or Acta Crystallographica Section E, ONLY the codes indicated for use with these journals should be used.
Alias: _publ_requested_category (cif_core.dic, 2.0.1)
Type: line
Default value: FA
Enumeration values:
| Value | Detail |
|---|---|
FA |
Full article |
FI |
Full submission - inorganic (Acta C) |
FO |
Full submission - organic (Acta C) |
FM |
Full submission - metal-organic (Acta C) |
CI |
CIF-access paper - inorganic (Acta C) (no longer in use) |
CO |
CIF-access paper - organic (Acta C) (no longer in use) |
CM |
CIF-access paper - metal-organic (Acta C) (no longer in use) |
EI |
Electronic submission - inorganic (Acta E) |
EO |
Electronic submission - organic (Acta E) |
EM |
Electronic submission - metal-organic (Acta E) |
AD |
Addenda and Errata (Acta C, Acta E) |
SC |
Short communication |
Category: publ
Mandatory: no
The name of the co-editor whom the authors would like to handle the submitted manuscript.
Alias: _publ_requested_coeditor_name (cif_core.dic, 2.0.1)
Type: line
Category: publ
Mandatory: no
The name of the journal to which the manuscript is being submitted.
Alias: _publ_requested_journal (cif_core.dic, 2.0.1)
Type: line
Category: publ
Mandatory: no
The abstract section of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ.manuscript_processed.
Alias: _publ_section_abstract (cif_core.dic, 2.0.1)
Type: text
Category: publ
Mandatory: no
The acknowledgements section of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ.manuscript_processed.
Alias: _publ_section_acknowledgements (cif_core.dic, 2.0.1)
Type: text
Category: publ
Mandatory: no
The comment section of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ.manuscript_processed.
Alias: _publ_section_comment (cif_core.dic, 2.0.1)
Type: text
Category: publ
Mandatory: no
The discussion section of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ.manuscript_processed.
Alias: _publ_section_discussion (cif_core.dic, 2.0.1)
Type: text
Category: publ
Mandatory: no
The experimental section of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ.manuscript_processed. The _publ.section_exptl_prep, _publ.section_exptl_solution and _publ.section_exptl_refinement items are preferred for separating the chemical preparation, structure solution and refinement aspects of the description of the experiment.
Alias: _publ_section_experimental (cif_core.dic, 2.0.1)
Type: text
Category: publ
Mandatory: no
The experimental preparation section of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ.manuscript_processed.
Alias: _publ_section_exptl_prep (cif_core.dic, 2.0.1)
Type: text
Category: publ
Mandatory: no
The experimental refinement section of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ.manuscript_processed.
Alias: _publ_section_exptl_refinement (cif_core.dic, 2.0.1)
Type: text
Category: publ
Mandatory: no
The experimental solution section of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ.manuscript_processed.
Alias: _publ_section_exptl_solution (cif_core.dic, 2.0.1)
Type: text
Category: publ
Mandatory: no
The figure captions section of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ.manuscript_processed.
Alias: _publ_section_figure_captions (cif_core.dic, 2.0.1)
Type: text
Category: publ
Mandatory: no
The introduction section of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ.manuscript_processed.
Alias: _publ_section_introduction (cif_core.dic, 2.0.1)
Type: text
Category: publ
Mandatory: no
The references section of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ.manuscript_processed.
Alias: _publ_section_references (cif_core.dic, 2.0.1)
Type: text
Category: publ
Mandatory: no
The synopsis section of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ.manuscript_processed.
Alias: _publ_section_synopsis (cif_core.dic, 2.0.1)
Type: text
Category: publ
Mandatory: no
The table legends section of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ.manuscript_processed.
Alias: _publ_section_table_legends (cif_core.dic, 2.0.1)
Type: text
Category: publ
Mandatory: no
The title of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ.manuscript_processed.
Alias: _publ_section_title (cif_core.dic, 2.0.1)
Type: text
Category: publ
Mandatory: no
The footnote to the title of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ.manuscript_processed.
Alias: _publ_section_title_footnote (cif_core.dic, 2.0.1)
Type: text
Data items in the PUBL_AUTHOR category record details of the authors of a manuscript submitted for publication.
Mandatory: no
Keys: _publ_author.name
Groups: inclusive_group iucr_group
Examples:
| Example | Detail |
|---|---|
loop_
_publ_author.name
_publ_author.address
'Willis, Anthony C.'
; Research School of Chemistry
Australian National University
GPO Box 4
Canberra, A.C.T.
Australia 2601
;
|
Example 1 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. |
Category: publ_author
Mandatory: no
The address of a publication author. If there is more than one author this is looped with _publ_author.name.
Alias: _publ_author_address (cif_core.dic, 2.0.1)
Type: text
Example:
Department
Institute
Street
City and postcode
COUNTRY
Category: publ_author
Mandatory: no
The e-mail address of a publication author. If there is more than one author, this will be looped with _publ_author.name. The format of e-mail addresses is given in Section 3.4, Address Specification, of Internet Message Format, RFC 2822, P. Resnick (Editor), Network Standards Group, April 2001.
Alias: _publ_author_email (cif_core.dic, 2.3.1)
Type: text
Examples:
| Example | Detail |
|---|---|
name@host.domain.country |
|
bm@iucr.org |
Category: publ_author
Mandatory: no
A footnote accompanying an author's name in the list of authors of a paper. Typically indicates sabbatical address, additional affiliations or date of decease.
Alias: _publ_author_footnote (cif_core.dic, 2.0.1)
Type: line
Examples:
| Example | Detail |
|---|---|
On leave from U. Western Australia |
|
Also at Department of Biophysics |
Category: publ_author
Mandatory: yes
The name of a publication author. If there are multiple authors this will be looped with _publ_author.address. The family name(s), followed by a comma and including any dynastic components, precedes the first names or initials.
Alias: _publ_author_name (cif_core.dic, 2.0.1)
Type: line
Examples:
| Example | Detail |
|---|---|
Bleary, Percival R. |
|
O'Neil, F.K. |
|
Van den Bossche, G. |
|
Yang, D.-L. |
|
Simonov, Yu.A. |
Data items in the PUBL_BODY category permit the labelling of different text sections within the body of a paper. Note that these should not be used in a paper which has a standard format with sections tagged by specific data names (such as in Acta Crystallographica Section C). Typically, each journal will supply a list of the specific items it requires in its Notes for Authors.
Mandatory: no
Keys: _publ_body.element _publ_body.label
Groups: inclusive_group iucr_group
Examples:
| Example | Detail |
|---|---|
loop_
_publ_body.element
_publ_body.label
_publ_body.title
_publ_body.format
_publ_body.contents
section 1 Introduction cif
; X-ray diffraction from a crystalline material provides
information on the thermally and spatially averaged
electron density in the crystal...
;
section 2 Theory tex
; In the rigid-atom approximation, the dynamic electron
density of an atom is described by the convolution
product of the static atomic density and a probability
density function,
$\rho_{dyn}(\bf r) = \rho_{stat}(\bf r) * P(\bf r). \eqno(1)$
;
|
Example 1 - based on a paper by R. Restori & D. Schwarzenbach [Acta Cryst. (1996), A52, 369-378]. |
loop_
_publ_body.element
_publ_body.label
_publ_body.title
_publ_body.contents
section 3
; The two-channel method for retrieval of the deformation
electron density
;
.
subsection 3.1 'The two-channel entropy S[\D\r(r)]'
; As the wide dynamic range involved in the total electron
density...
;
subsection 3.2
'Uniform vs informative prior model densities' .
subsubsection 3.2.1 'Use of uniform models'
; Straightforward algebra leads to expressions analogous
to...
;
|
Example 2 - based on a paper by R. J. Papoular, Y. Vekhter & P. Coppens [Acta Cryst. (1996), A52, 397-407]. |
Category: publ_body
Mandatory: no
A text section of a paper.
Alias: _publ_body_contents (cif_core.dic, 2.0.1)
Type: text
Category: publ_body
Mandatory: no
The functional role of the associated text section.
Alias: _publ_body_element (cif_core.dic, 2.0.1)
Type: code
Enumeration values:
| Value | Detail |
|---|---|
section |
|
subsection |
|
subsubsection |
|
appendix |
|
footnote |
Category: publ_body
Mandatory: no
Code indicating the appropriate typesetting conventions for accented characters and special symbols in the text section.
Alias: _publ_body_format (cif_core.dic, 2.0.1)
Type: code
Enumeration values:
| Value | Detail |
|---|---|
ascii |
no coding for special symbols |
cif |
CIF convention |
latex |
LaTeX |
sgml |
SGML (ISO 8879) |
tex |
TeX |
troff |
troff or nroff |
Category: publ_body
Mandatory: no
Code identifying the section of text.
Alias: _publ_body_label (cif_core.dic, 2.0.1)
Type: code
Examples:
| Example | Detail |
|---|---|
1 |
|
1.1 |
|
2.1.3 |
Category: publ_body
Mandatory: no
Title of the associated section of text.
Alias: _publ_body_title (cif_core.dic, 2.0.1)
Type: text
Data items in the PUBL_MANUSCRIPT_INCL category allow the authors of a manuscript submitted for publication to list data names that should be added to the standard request list used by the journal printing software.
Mandatory: no
Keys: _publ_manuscript_incl.entry_id
Groups: inclusive_group iucr_group
Examples:
| Example | Detail |
|---|---|
_publ_manuscript_incl.entry_id 'EXAMHYPO'
loop_
_publ_manuscript_incl.extra_item
_publ_manuscript_incl.extra_info
_publ_manuscript_incl.extra_defn
'_atom_site.symmetry_multiplicity'
'to emphasise special sites' yes
'_chemical.compound_source'
'rare material, unusual source' yes
'_reflns.d_resolution_high'
'limited data is a problem here' yes
'_crystal.magnetic_permeability'
'unusual value for this material' no
|
Example 1 - hypothetical example. |
Mandatory: yes
This data item is a pointer to _entry.id in the ENTRY category.
Category: publ_manuscript_incl
Mandatory: no
Flags whether the corresponding data item marked for inclusion in a journal request list is a standard CIF definition or not.
Alias: _publ_manuscript_incl_extra_defn (cif_core.dic, 2.0.1)
Type: line
Enumeration values:
| Value | Detail |
|---|---|
no |
not a standard CIF data name |
n |
abbreviation for "no" |
yes |
a standard CIF data name |
y |
abbreviation for "yes" |
Category: publ_manuscript_incl
Mandatory: no
A short note indicating the reason why the author wishes the corresponding data item marked for inclusion in the journal request list to be published.
Alias: _publ_manuscript_incl_extra_info (cif_core.dic, 2.0.1)
Type: text
Examples:
| Example | Detail |
|---|---|
to emphasise very special sites |
|
rare material from unusual source |
|
the limited data is a problem here |
|
a new data quantity needed here |
Category: publ_manuscript_incl
Mandatory: no
Specifies the inclusion of specific data into a manuscript which are not normally requested by the journal. The values of this item are the extra data names (which MUST be enclosed in single quotes) that will be added to the journal request list.
Alias: _publ_manuscript_incl_extra_item (cif_core.dic, 2.0.1)
Type: line
Examples:
| Example | Detail |
|---|---|
_atom_site.symmetry_multiplicity |
|
_chemical.compound_source |
|
_reflns.d_resolution_high |
|
_crystal.magnetic_permeability |
Data items in the REFINE category record details about the structure-refinement parameters.
Mandatory: no
Keys: _refine.entry_id
Groups: inclusive_group refine_group
Examples:
| Example | Detail |
|---|---|
_refine.entry_id '5HVP'
_refine.ls_number_reflns_obs 12901
_refine.ls_number_restraints 6609
_refine.ls_number_parameters 7032
_refine.ls_R_Factor_obs 0.176
_refine.ls_weighting_scheme calc
_refine.ls_weighting_details
; Sigdel model of Konnert-Hendrickson:
Sigdel: Afsig + Bfsig*(sin(theta)/lambda-1/6)
Afsig = 22.0, Bfsig = -150.0 at beginning of refinement
Afsig = 15.5, Bfsig = -50.0 at end of refinement
;
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
_refine.details sfls:_F_calc_weight_full_matrix
_refine.ls_structure_factor_coef F
_refine.ls_matrix_type full
_refine.ls_weighting_scheme calc
_refine.ls_weighting_details 'w=1/(\s^2^(F)+0.0004F^2^)'
_refine.ls_hydrogen_treatment 'refxyz except H332B noref'
_refine.ls_extinction_method Zachariasen
_refine.ls_extinction_coef 3514
_refine.ls_extinction_expression
; Larson, A. C. (1970). "Crystallographic Computing", edited
by F. R. Ahmed. Eq. (22) p. 292. Copenhagen: Munksgaard.
_refine.ls_abs_structure_details
; The absolute configuration was assigned to agree with the
known chirality at C3 arising from its precursor l-leucine.
;
_refine.ls_abs_structure_Flack 0
_refine.ls_number_reflns_obs 1408
_refine.ls_number_parameters 272
_refine.ls_number_restraints 0
_refine.ls_number_constraints 0
_refine.ls_R_factor_all .038
_refine.ls_R_factor_obs .034
_refine.ls_wR_factor_all .044
_refine.ls_wR_factor_obs .042
_refine.ls_goodness_of_fit_all 1.462
_refine.ls_goodness_of_fit_obs 1.515
_refine.ls_shift_over_esd_max .535
_refine.ls_shift_over_esd_mean .044
_refine.diff_density_min -.108
_refine.diff_density_max .131
|
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. |
Category: refine
Mandatory: no
Sub-category: matrix
The [1][1] element of the matrix that defines the overall anisotropic displacement model if one was refined for this structure.
Type: float
Units: angstroms_squared
Category: refine
Mandatory: no
Sub-category: matrix
The [1][2] element of the matrix that defines the overall anisotropic displacement model if one was refined for this structure.
Type: float
Units: angstroms_squared
Category: refine
Mandatory: no
Sub-category: matrix
The [1][3] element of the matrix that defines the overall anisotropic displacement model if one was refined for this structure.
Type: float
Units: angstroms_squared
Category: refine
Mandatory: no
Sub-category: matrix
The [2][2] element of the matrix that defines the overall anisotropic displacement model if one was refined for this structure.
Type: float
Units: angstroms_squared
Category: refine
Mandatory: no
Sub-category: matrix
The [2][3] element of the matrix that defines the overall anisotropic displacement model if one was refined for this structure.
Type: float
Units: angstroms_squared
Category: refine
Mandatory: no
Sub-category: matrix
The [3][3] element of the matrix that defines the overall anisotropic displacement model if one was refined for this structure.
Type: float
Units: angstroms_squared
Category: refine
Mandatory: no
The maximum isotropic displacement parameter (B value) found in the coordinate set.
Type: float
Units: angstroms_squared
Category: refine
Mandatory: no
The mean isotropic displacement parameter (B value) for the coordinate set.
Type: float
Units: angstroms_squared
Category: refine
Mandatory: no
The minimum isotropic displacement parameter (B value) found in the coordinate set.
Type: float
Units: angstroms_squared
Category: refine
Mandatory: no
The correlation coefficient between the observed and calculated structure factors for reflections included in the refinement. The correlation coefficient is scale-independent and gives an idea of the quality of the refined model. sumi(Foi Fci - <Fo><Fc>) Rcorr = ------------------------------------------------------------ SQRT{sumi(Foi)2-<Fo>2} SQRT{sumi(Fci)2-<Fc>2} Fo = observed structure factors Fc = calculated structure factors <> denotes average value summation is over reflections included in the refinement
Alias: _refine.ebi_Correlation_coeff_Fo_to_Fc (ebi_extensions, 1.0)
Type: float
Category: refine
Mandatory: no
The correlation coefficient between the observed and calculated structure factors for reflections not included in the refinement (free reflections). The correlation coefficient is scale-independent and gives an idea of the quality of the refined model. sumi(Foi Fci - <Fo><Fc>) Rcorr = ------------------------------------------------------------ SQRT{sumi(Foi)2-<Fo>2} SQRT{sumi(Fci)2-<Fc>2} Fo = observed structure factors Fc = calculated structure factors <> denotes average value summation is over reflections not included in the refinement (free reflections)
Alias: _refine.ebi_Correlation_coeff_Fo_to_Fc_free (ebi_extensions, 1.0)
Type: float
Category: refine
Mandatory: no
Description of special aspects of the refinement process.
Alias: _refine_special_details (cif_core.dic, 2.0.1)
Type: text
Category: refine
Mandatory: no
The maximum value of the electron density in the final difference Fourier map.
Alias: _refine_diff_density_max (cif_core.dic, 2.0.1)
Type: float
Type conditions: esd
Units: electrons_per_angstroms_cubed
Related item: _refine.diff_density_max_esd (associated_esd)
Category: refine
Mandatory: no
The standard uncertainty (estimated standard deviation) of _refine.diff_density_max.
Type: float
Units: electrons_per_angstroms_cubed
Related item: _refine.diff_density_max (associated_value)
Category: refine
Mandatory: no
The minimum value of the electron density in the final difference Fourier map.
Alias: _refine_diff_density_min (cif_core.dic, 2.0.1)
Type: float
Type conditions: esd
Units: electrons_per_angstroms_cubed
Related item: _refine.diff_density_min_esd (associated_esd)
Category: refine
Mandatory: no
The standard uncertainty (estimated standard deviation) of _refine.diff_density_min.
Type: float
Units: electrons_per_angstroms_cubed
Related item: _refine.diff_density_min (associated_value)
Category: refine
Mandatory: no
The root-mean-square-deviation of the electron density in the final difference Fourier map. This value is measured with respect to the arithmetic mean density and is derived from summations over each grid point in the asymmetric unit of the cell. This quantity is useful for assessing the significance of the values of _refine.diff_density_min and _refine.diff_density_max, and also for defining suitable contour levels.
Alias: _refine_diff_density_rms (cif_core.dic, 2.0.1)
Type: float
Type conditions: esd
Units: electrons_per_angstroms_cubed
Related item: _refine.diff_density_rms_esd (associated_esd)
Category: refine
Mandatory: no
The standard uncertainty (estimated standard deviation) of _refine.diff_density_rms.
Type: float
Units: electrons_per_angstroms_cubed
Related item: _refine.diff_density_rms (associated_value)
Mandatory: yes
This data item is a pointer to _entry.id in the ENTRY category.
Category: refine
Mandatory: no
The nature of the absolute structure and how it was determined. For example, this may describe the Friedel pairs used.
Alias: _refine_ls_abs_structure_details (cif_core.dic, 2.0.1)
Type: text
Category: refine
Mandatory: no
The measure of absolute structure (enantiomorph or polarity) as defined by Flack (1983). For centrosymmetric structures, the only permitted value, if the data name is present, is 'inapplicable', represented by '.' . For noncentrosymmetric structures the value must lie in the 99.97% Gaussian confidence interval -3u =< x =< 1 + 3u and a standard uncertainty (estimated standard deviation) u must be supplied. The item range of [0.0:1.0] is correctly interpreted as meaning (0.0 - 3u) =< x =< (1.0 + 3u). Ref: Flack, H. D. (1983). Acta Cryst. A39, 876-881.
Alias: _refine_ls_abs_structure_Flack (cif_core.dic, 2.0.1)
Type: float
Type conditions: esd
Related item: _refine.ls_abs_structure_Flack_esd (associated_esd)
Range: [1.0, 1.0] [0.0, 1.0] [0.0, 0.0]
Category: refine
Mandatory: no
The standard uncertainty (estimated standard deviation) of _refine.ls_abs_structure_Flack.
Type: float
Related item: _refine.ls_abs_structure_Flack (associated_value)
Category: refine
Mandatory: no
The measure of absolute structure (enantiomorph or polarity) as defined by Rogers. The value must lie in the 99.97% Gaussian confidence interval -1 -3u =< η =< 1 + 3u and a standard uncertainty (estimated standard deviation) u must be supplied. The item range of [-1.0, 1.0] is correctly interpreted as meaning (-1.0 - 3u) =< η =< (1.0 + 3u). Ref: Rogers, D. (1981). Acta Cryst. A37, 734-741.
Alias: _refine_ls_abs_structure_Rogers (cif_core.dic, 2.0.1)
Type: float
Type conditions: esd
Related item: _refine.ls_abs_structure_Rogers_esd (associated_esd)
Range: [1.0, 1.0] [-1.0, 1.0] [-1.0, -1.0]
Category: refine
Mandatory: no
The standard uncertainty (estimated standard deviation) of _refine.ls_abs_structure_Rogers.
Type: float
Related item: _refine.ls_abs_structure_Rogers (associated_value)
Category: refine
Mandatory: yes
The smallest value for the interplanar spacings for the reflection data used in the refinement in angstroms. This is called the highest resolution.
Alias: _refine_ls_d_res_high (cif_core.dic, 2.0.1)
Type: float
Units: angstroms
Range: [0.0, .] [0.0, 0.0]
Category: refine
Mandatory: yes
The largest value for the interplanar spacings for the reflection data used in the refinement in angstroms. This is called the lowest resolution.
Alias: _refine_ls_d_res_low (cif_core.dic, 2.0.1)
Type: float
Units: angstroms
Range: [0.0, .] [0.0, 0.0]
Category: refine
Mandatory: no
The extinction coefficient used to calculate the correction factor applied to the structure-factor data. The nature of the extinction coefficient is given in the definitions of _refine.ls_extinction_expression and _refine.ls_extinction_method. For the 'Zachariasen' method it is the r* value; for the 'Becker-Coppens type 1 isotropic' method it is the 'g' value, and for 'Becker-Coppens type 2 isotropic' corrections it is the 'rho' value. Note that the magnitude of these values is usually of the order of 10000. Ref: Becker, P. J. & Coppens, P. (1974). Acta Cryst. A30, 129-47, 148-153. Zachariasen, W. H. (1967). Acta Cryst. 23, 558-564. Larson, A. C. (1967). Acta Cryst. 23, 664-665.
Alias: _refine_ls_extinction_coef (cif_core.dic, 2.0.1)
Type: float
Type conditions: esd
Related item: _refine.ls_extinction_coef_esd (associated_esd)
Example:
3472
Zachariasen coefficient r* = 0.347 E04
Category: refine
Mandatory: no
The standard uncertainty (estimated standard deviation) of _refine.ls_extinction_coef.
Type: float
Related item: _refine.ls_extinction_coef (associated_value)
Category: refine
Mandatory: no
A description of or reference to the extinction-correction equation used to apply the data item _refine.ls_extinction_coef. This information must be sufficient to reproduce the extinction-correction factors applied to the structure factors.
Alias: _refine_ls_extinction_expression (cif_core.dic, 2.0.1)
Type: text
Example:
Larson, A. C. (1970). "Crystallographic Computing", edited by
F. R. Ahmed. Eq. (22), p.292. Copenhagen: Munksgaard.
Category: refine
Mandatory: no
A description of the extinction-correction method applied. This description should include information about the correction method, either 'Becker-Coppens' or 'Zachariasen'. The latter is sometimes referred to as the 'Larson' method even though it employs Zachariasen's formula. The Becker-Coppens procedure is referred to as 'type 1' when correcting secondary extinction dominated by the mosaic spread; as 'type 2' when secondary extinction is dominated by particle size and includes a primary extinction component; and as 'mixed' when there is a mixture of types 1 and 2. For the Becker-Coppens method, it is also necessary to set the mosaic distribution as either 'Gaussian' or 'Lorentzian' and the nature of the extinction as 'isotropic' or 'anisotropic'. Note that if either the 'mixed' or 'anisotropic' corrections are applied, the multiple coefficients cannot be contained in *_extinction_coef and must be listed in _refine.details. Ref: Becker, P. J. & Coppens, P. (1974). Acta Cryst. A30, 129-147, 148-153. Zachariasen, W. H. (1967). Acta Cryst. 23, 558- 564. Larson, A. C. (1967). Acta Cryst. 23, 664-665.
Alias: _refine_ls_extinction_method (cif_core.dic, 2.0.1)
Type: text
Example:
B-C type 2 Gaussian isotropic
Category: refine
Mandatory: no
The least-squares goodness-of-fit parameter S for all data after the final cycle of refinement. Ideally, account should be taken of parameters restrained in the least-squares refinement. See also the definition of _refine.ls_restrained_S_all. ( sum|w |Yobs - Ycalc|2| )1/2 S = ( ---------------------------- ) ( Nref - Nparam ) Yobs = the observed coefficients (see _refine.ls_structure_factor_coef) Ycalc = the calculated coefficients (see _refine.ls_structure_factor_coef) w = the least-squares reflection weight [1/(e.s.d. squared)] Nref = the number of reflections used in the refinement Nparam = the number of refined parameters sum is taken over the specified reflections
Alias: _refine_ls_goodness_of_fit_all (cif_core.dic, 2.0.1)
Type: float
Type conditions: esd
Related item: _refine.ls_goodness_of_fit_all_esd (associated_esd)
Range: [0.0, .] [0.0, 0.0]
Category: refine
Mandatory: no
The standard uncertainty (estimated standard deviation) of _refine.ls_goodness_of_fit_all.
Type: float
Related item: _refine.ls_goodness_of_fit_all (associated_value)
Category: refine
Mandatory: no
The least-squares goodness-of-fit parameter S for reflection data classified as 'observed' (see _reflns.observed_criterion) after the final cycle of refinement. Ideally, account should be taken of parameters restrained in the least-squares refinement. See also the definition of _refine.ls_restrained_S_obs. ( sum|w |Yobs - Ycalc|2| )1/2 S = ( ---------------------------- ) ( Nref - Nparam ) Yobs = the observed coefficients (see _refine.ls_structure_factor_coef) Ycalc = the calculated coefficients (see _refine.ls_structure_factor_coef) w = the least-squares reflection weight [1/(e.s.d. squared)] Nref = the number of reflections used in the refinement Nparam = the number of refined parameters sum is taken over the specified reflections
Alias: _refine_ls_goodness_of_fit_obs (cif_core.dic, 2.0.1)
Type: float
Type conditions: esd
Related item: _refine.ls_goodness_of_fit_obs_esd (associated_esd)
Range: [0.0, .] [0.0, 0.0]
Category: refine
Mandatory: no
The standard uncertainty (estimated standard deviation) of _refine.ls_goodness_of_fit_obs.
Type: float
Related item: _refine.ls_goodness_of_fit_obs (associated_value)
Category: refine
Mandatory: no
Treatment of hydrogen atoms in the least-squares refinement.
Alias: _refine_ls_hydrogen_treatment (cif_core.dic, 2.0.1)
Type: ucode
Enumeration values:
| Value | Detail |
|---|---|
refall |
refined all H-atom parameters |
refxyz |
refined H-atom coordinates only |
refU |
refined H-atom U's only |
noref |
no refinement of H-atom parameters |
constr |
H-atom parameters constrained |
mixed |
some constrained, some independent |
undef |
H-atom parameters not defined |
Category: refine
Mandatory: no
Type of matrix used to accumulate the least-squares derivatives.
Alias: _refine_ls_matrix_type (cif_core.dic, 2.0.1)
Type: ucode
Enumeration values:
| Value | Detail |
|---|---|
full |
full |
fullcycle |
full with fixed elements per cycle |
atomblock |
block diagonal per atom |
userblock |
user-defined blocks |
diagonal |
diagonal elements only |
sparse |
selected elements only |
Category: refine
Mandatory: no
The number of constrained (non-refined or dependent) parameters in the least-squares process. These may be due to symmetry or any other constraint process (e.g. rigid-body refinement). See also _atom_site.constraints and _atom_site.refinement_flags. A general description of constraints may appear in _refine.details.
Alias: _refine_ls_number_constraints (cif_core.dic, 2.0.1)
Type: int
Range: [0, .] [0, 0]
Category: refine
Mandatory: no
The number of parameters refined in the least-squares process. If possible, this number should include some contribution from the restrained parameters. The restrained parameters are distinct from the constrained parameters (where one or more parameters are linearly dependent on the refined value of another). Least-squares restraints often depend on geometry or energy considerations and this makes their direct contribution to this number, and to the goodness-of-fit calculation, difficult to assess.
Alias: _refine_ls_number_parameters (cif_core.dic, 2.0.1)
Type: int
Range: [0, .] [0, 0]
Category: refine
Mandatory: no
The number of reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low.
Type: int
Range: [0, .] [0, 0]
Category: refine
Mandatory: no
The number of reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion.
Alias: _refine_ls_number_reflns (cif_core.dic, 2.0.1)
Type: int
Range: [0, .] [0, 0]
Category: refine
Mandatory: no
The number of reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details.
Type: int
Range: [0, .] [0, 0]
Category: refine
Mandatory: no
The number of reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the working reflections (i.e. were included in the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details.
Type: int
Range: [0, .] [0, 0]
Category: refine
Mandatory: no
The number of restrained parameters. These are parameters which are not directly dependent on another refined parameter. Restrained parameters often involve geometry or energy dependencies. See also _atom_site.constraints and _atom_site.refinement_flags. A general description of refinement constraints may appear in _refine.details.
Alias: _refine_ls_number_restraints (cif_core.dic, 2.0.1)
Type: int
Range: [0, .] [0, 0]
Category: refine
Mandatory: no
The number of reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion, expressed as a percentage of the number of geometrically observable reflections that satisfy the resolution limits.
Type: float
Category: refine
Mandatory: no
The number of reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor, expressed as a percentage of the number of geometrically observable reflections that satisfy the resolution limits.
Type: float
Category: refine
Mandatory: no
Residual factor R for all reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low. sum|Fobs - Fcalc| R = --------------------- sum|Fobs| Fobs = the observed structure-factor amplitudes Fcalc = the calculated structure-factor amplitudes sum is taken over the specified reflections
Alias: _refine_ls_R_factor_all (cif_core.dic, 2.0.1)
Type: float
Related item: _refine.ls_wR_factor_all (alternate)
Range: [0.0, .] [0.0, 0.0]
Category: refine
Mandatory: no
Residual factor R for reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion. _refine.ls_R_factor_obs should not be confused with _refine.ls_R_factor_R_work; the former reports the results of a refinement in which all observed reflections were used, the latter a refinement in which a subset of the observed reflections were excluded from refinement for the calculation of a 'free' R factor. However, it would be meaningful to quote both values if a 'free' R factor were calculated for most of the refinement, but all of the observed reflections were used in the final rounds of refinement; such a protocol should be explained in _refine.details. sum|Fobs - Fcalc| R = --------------------- sum|Fobs| Fobs = the observed structure-factor amplitudes Fcalc = the calculated structure-factor amplitudes sum is taken over the specified reflections
Alias: _refine_ls_R_factor_obs (cif_core.dic, 2.0.1)
Type: float
Related item: _refine.ls_wR_factor_obs (alternate)
Range: [0.0, .] [0.0, 0.0]
Category: refine
Mandatory: no
Residual factor R for reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details. sum|Fobs - Fcalc| R = --------------------- sum|Fobs| Fobs = the observed structure-factor amplitudes Fcalc = the calculated structure-factor amplitudes sum is taken over the specified reflections
Type: float
Related items: _refine.ls_wR_factor_R_free (alternate) _refine.ls_R_factor_R_free_error (associated_error)
Range: [0.0, .] [0.0, 0.0]
Category: refine
Mandatory: no
The estimated error in _refine.ls_R_factor_R_free. The method used to estimate the error is described in the item _refine.ls_R_factor_R_free_error_details.
Type: float
Related item: _refine.ls_R_factor_R_free (associated_value)
Category: refine
Mandatory: no
Special aspects of the method used to estimated the error in _refine.ls_R_factor_R_free.
Type: text
Category: refine
Mandatory: no
Residual factor R for reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the working reflections (i.e. were included in the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details. _refine.ls_R_factor_obs should not be confused with _refine.ls_R_factor_R_work; the former reports the results of a refinement in which all observed reflections were used, the latter a refinement in which a subset of the observed reflections were excluded from refinement for the calculation of a 'free' R factor. However, it would be meaningful to quote both values if a 'free' R factor were calculated for most of the refinement, but all of the observed reflections were used in the final rounds of refinement; such a protocol should be explained in _refine.details. sum|Fobs - Fcalc| R = --------------------- sum|Fobs| Fobs = the observed structure-factor amplitudes Fcalc = the calculated structure-factor amplitudes sum is taken over the specified reflections
Type: float
Related item: _refine.ls_wR_factor_R_work (alternate)
Range: [0.0, .] [0.0, 0.0]
Category: refine
Mandatory: no
Residual factor R(Fsqd) for reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion, calculated on the squares of the observed and calculated structure-factor amplitudes. sum|Fobs2 - Fcalc2| R(Fsqd) = --------------------------- sum|Fobs2| Fobs2 = squares of the observed structure-factor amplitudes Fcalc2 = squares of the calculated structure-factor amplitudes sum is taken over the specified reflections
Alias: _refine_ls_R_Fsqd_factor (cif_core.dic, 2.0.1)
Type: float
Range: [0.0, .] [0.0, 0.0]
Category: refine
Mandatory: no
Residual factor R(I) for reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion, calculated on the estimated reflection intensities. This is most often calculated in Rietveld refinements against powder data, where it is referred to as RB or RBragg. sum|Iobs - Icalc| R(I) = --------------------- sum|Iobs| Iobs = the net observed intensities Icalc = the net calculated intensities sum is taken over the specified reflections
Alias: _refine_ls_R_I_factor (cif_core.dic, 2.0.1)
Type: float
Range: [0.0, .] [0.0, 0.0]
Category: refine
Mandatory: no
The ratio of the total number of observations of the reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low to the number of crystallographically unique reflections that satisfy the same limits.
Type: float
Category: refine
Mandatory: no
The ratio of the total number of observations of the reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion to the number of crystallographically unique reflections that satisfy the same limits.
Type: float
Category: refine
Mandatory: no
The least-squares goodness-of-fit parameter S' for all reflections after the final cycle of least-squares refinement. This parameter explicitly includes the restraints applied in the least-squares process. See also the definition of _refine.ls_goodness_of_fit_all. ( sum |w |Yobs - Ycalc|2| )1/2 ( + sumr|wr |Pcalc - Ptarg|2| ) S' = ( ------------------------------------- ) ( Nref + Nrestr - Nparam ) Yobs = the observed coefficients (see _refine.ls_structure_factor_coef) Ycalc = the calculated coefficients (see _refine.ls_structure_factor_coef) w = the least-squares reflection weight [1/(e.s.d. squared)] Pcalc = the calculated restraint values Ptarg = the target restraint values wr = the restraint weight Nref = the number of reflections used in the refinement (see _refine.ls_number_reflns_obs) Nrestr = the number of restraints (see _refine.ls_number_restraints) Nparam = the number of refined parameters (see _refine.ls_number_parameters) sum is taken over the specified reflections sumr is taken over the restraints
Alias: _refine_ls_restrained_S_all (cif_core.dic, 2.0.1)
Type: float
Range: [0.0, .] [0.0, 0.0]
Category: refine
Mandatory: no
The least-squares goodness-of-fit parameter S' for reflection data classified as observed (see _reflns.observed_criterion) after the final cycle of least-squares refinement. This parameter explicitly includes the restraints applied in the least-squares process. See also the definition of _refine.ls_goodness_of_fit_obs. ( sum |w |Yobs - Ycalc|2| )1/2 ( + sumr|wr |Pcalc - Ptarg|2| ) S' = ( ------------------------------------- ) ( Nref + Nrestr - Nparam ) Yobs = the observed coefficients (see _refine.ls_structure_factor_coef) Ycalc = the calculated coefficients (see _refine.ls_structure_factor_coef) w = the least-squares reflection weight [1/(e.s.d. squared)] Pcalc = the calculated restraint values Ptarg = the target restraint values wr = the restraint weight Nref = the number of reflections used in the refinement (see _refine.ls_number_reflns_obs) Nrestr = the number of restraints (see _refine.ls_number_restraints) Nparam = the number of refined parameters (see _refine.ls_number_parameters) sum is taken over the specified reflections sumr is taken over the restraints
Alias: _refine_ls_restrained_S_obs (cif_core.dic, 2.0.1)
Type: float
Range: [0.0, .] [0.0, 0.0]
Category: refine
Mandatory: no
The largest ratio of the final least-squares parameter shift to the final standard uncertainty (estimated standard deviation).
Alias: _refine_ls_shift/esd_max (cif_core.dic, 2.0.1)
Type: float
Range: [0.0, .] [0.0, 0.0]
Category: refine
Mandatory: no
The average ratio of the final least-squares parameter shift to the final standard uncertainty (estimated standard deviation).
Alias: _refine_ls_shift/esd_mean (cif_core.dic, 2.0.1)
Type: float
Range: [0.0, .] [0.0, 0.0]
Category: refine
Mandatory: no
Structure-factor coefficient |F|, F2 or I used in the least- squares refinement process.
Alias: _refine_ls_structure_factor_coef (cif_core.dic, 2.0.1)
Type: ucode
Enumeration values:
| Value | Detail |
|---|---|
F |
structure-factor magnitude |
Fsqd |
structure factor squared |
Inet |
net intensity |
Category: refine
Mandatory: no
A description of special aspects of the weighting scheme used in least-squares refinement. Used to describe the weighting when the value of _refine.ls_weighting_scheme is specified as 'calc'.
Alias: _refine_ls_weighting_details (cif_core.dic, 2.0.1)
Type: text
Example:
Sigdel model of Konnert-Hendrickson:
Sigdel =
Afsig + Bfsig*(sin(theta)/lambda-1/6)
Afsig = 22.0, Bfsig = 150.0
at the beginning of refinement.
Afsig = 16.0, Bfsig = 60.0
at the end of refinement.
Category: refine
Mandatory: no
The weighting scheme applied in the least-squares process. The standard code may be followed by a description of the weight (but see _refine.ls_weighting_details for a preferred approach).
Alias: _refine_ls_weighting_scheme (cif_core.dic, 2.0.1)
Type: ucode
Enumeration values:
| Value | Detail |
|---|---|
sigma |
based on measured e.s.d.'s |
unit |
unit or no weights applied |
calc |
calculated weights applied |
Category: refine
Mandatory: no
Weighted residual factor wR for all reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low. ( sum|w |Yobs - Ycalc|2| )1/2 wR = ( ---------------------------- ) ( sum|w Yobs2| ) Yobs = the observed amplitude specified by _refine.ls_structure_factor_coef Ycalc = the calculated amplitude specified by _refine.ls_structure_factor_coef w = the least-squares weight sum is taken over the specified reflections
Alias: _refine_ls_wR_factor_all (cif_core.dic, 2.0.1)
Type: float
Related item: _refine.ls_R_factor_all (alternate)
Range: [0.0, .] [0.0, 0.0]
Category: refine
Mandatory: no
Weighted residual factor wR for reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion. ( sum|w |Yobs - Ycalc|2| )1/2 wR = ( ---------------------------- ) ( sum|w Yobs2| ) Yobs = the observed amplitude specified by _refine.ls_structure_factor_coef Ycalc = the calculated amplitude specified by _refine.ls_structure_factor_coef w = the least-squares weight sum is taken over the specified reflections
Alias: _refine_ls_wR_factor_obs (cif_core.dic, 2.0.1)
Type: float
Related item: _refine.ls_R_factor_obs (alternate)
Range: [0.0, .] [0.0, 0.0]
Category: refine
Mandatory: no
Weighted residual factor wR for reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details. ( sum|w |Yobs - Ycalc|2| )1/2 wR = ( ---------------------------- ) ( sum|w Yobs2| ) Yobs = the observed amplitude specified by _refine.ls_structure_factor_coef Ycalc = the calculated amplitude specified by _refine.ls_structure_factor_coef w = the least-squares weight sum is taken over the specified reflections
Type: float
Related item: _refine.ls_R_factor_R_free (alternate)
Range: [0.0, .] [0.0, 0.0]
Category: refine
Mandatory: no
Weighted residual factor wR for reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the working reflections (i.e. were included in the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details. ( sum|w |Yobs - Ycalc|2| )1/2 wR = ( ---------------------------- ) ( sum|w Yobs2| ) Yobs = the observed amplitude specified by _refine.ls_structure_factor_coef Ycalc = the calculated amplitude specified by _refine.ls_structure_factor_coef w = the least-squares weight sum is taken over the specified reflections
Type: float
Related item: _refine.ls_R_factor_R_work (alternate)
Range: [0.0, .] [0.0, 0.0]
Category: refine
Mandatory: no
The maximum value for occupancy found in the coordinate set.
Type: float
Range: [0.0, .] [0.0, 0.0]
Category: refine
Mandatory: no
The minimum value for occupancy found in the coordinate set.
Type: float
Range: [0.0, .] [0.0, 0.0]
Category: refine
Mandatory: no
The overall standard uncertainty (estimated standard deviation)
of the displacement parameters based on a maximum-likelihood
residual.
The overall standard uncertainty (sigmaB)2 gives an idea
of the uncertainty in the B values of averagely defined
atoms (atoms with B values equal to the average B value).
N_a
(sigma~B~)2 = 8 ----------------------------------------------
sumi {[1/Sigma - (E_o)2 (1-m2)](SUM_AS)s4}
SUM_AS = (sigma_A)2/Sigma2
N_a = number of atoms
Sigma = (sigma_{E;exp})2 + epsilon [1-(sigma_A)2]
E_o = normalized structure factors
sigma_{E;exp} = experimental uncertainties of normalized
structure factors
sigma_A =
Alias: _refine.ebi_Overall_ESU_B (ebi_extensions, 1.0)
Type: float
Category: refine
Mandatory: no
The overall standard uncertainty (estimated standard deviation) of the positional parameters based on a maximum likelihood residual. The overall standard uncertainty (sigmaX)2 gives an idea of the uncertainty in the position of averagely defined atoms (atoms with B values equal to average B value) 3 N_a (sigma~X~)2 = ----------------------------------------------------- 8 pi2 sum~i~ {[1/Sigma - (E_o)2 (1-m2)](SUM_AS)s2} SUM_AS = (sigma_A)2/Sigma2) N_a = number of atoms Sigma = (sigma_{E;exp})2 + epsilon [1-{sigma_A)2] E_o = normalized structure factors sigma_{E;exp} = experimental uncertainties of normalized structure factors sigma_A = <cos 2 pi s delta_x> SQRT(Sigma_P/Sigma_N) estimated using maximum likelihood Sigma_P = sum_{atoms in model} f2 Sigma_N = sum_{atoms in crystal} f2 f = form factor of atoms delta_x = expected error m = figure of merit of phases of reflections included in the summation s = reciprocal-space vector epsilon = multiplicity of the diffracting plane summation is over all reflections included in refinement Ref: (sigma_A estimation) "Refinement of macromolecular structures by the maximum-likelihood method", Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997). Acta Cryst. D53, 240-255. (SU ML estimation) Murshudov, G. N. & Dodson, E. J. (1997). Simplified error estimation a la Cruickshank in macromolecular crystallography. CCP4 Newsletter on Protein Crystallography, No. 33, January 1997, pp. 31-39. http://www.ccp4.ac.uk/newsletters/newsletter33/murshudov.html
Alias: _refine.ebi_Overall_ESU_ML (ebi_extensions, 1.0)
Type: float
Category: refine
Mandatory: no
The overall standard uncertainty (estimated standard deviation) of the displacement parameters based on the crystallographic R value, expressed in a formalism known as the dispersion precision indicator (DPI). The overall standard uncertainty (sigmaB) gives an idea of the uncertainty in the B values of averagely defined atoms (atoms with B values equal to the average B value). N_a (sigma_B)2 = 0.65 --------- (R_value)2 (D_min)2 C(-2/3) (N_o-N_p) N_a = number of atoms N_o = number of reflections included in refinement N_p = number of refined parameters R_value = conventional crystallographic R value D_min = maximum resolution C = completeness of data Ref: Cruickshank, D. W. J. (1999). Acta Cryst. D55, 583-601. Murshudov, G. N. & Dodson, E. J. (1997). Simplified error estimation a la Cruickshank in macromolecular crystallography. CCP4 Newsletter on Protein Crystallography, No. 33, January 1997, pp. 31-39. http://www.ccp4.ac.uk/newsletters/newsletter33/murshudov.html
Alias: _refine.ebi_Overall_ESU_R_Cruickshanks_DPI (ebi_extensions, 1.0)
Type: float
Category: refine
Mandatory: no
The overall standard uncertainty (estimated standard deviation) of the displacement parameters based on the free R value. The overall standard uncertainty gives an idea of the uncertainty in the B values of averagely defined atoms (atoms with B values equal to the average B value). N_a (sigma_B)2 = 0.65 ----- (R_free)2 (D_min)2 C(-2/3) N_o N_a = number of atoms N_o = number of reflections included in refinement R_free = conventional free crystallographic R value calculated using reflections not included in refinement D_min = maximum resolution C = completeness of data Ref: Cruickshank, D. W. J. (1999). Acta Cryst. D55, 583-601. Murshudov, G. N. & Dodson, E. J. (1997). Simplified error estimation a la Cruickshank in macromolecular crystallography. CCP4 Newsletter on Protein Crystallography, No. 33, January 1997, pp. 31-39. http://www.ccp4.ac.uk/newsletters/newsletter33/murshudov.html
Alias: _refine.ebi_Overall_ESU_Rfree (ebi_extensions, 1.0)
Type: float
Category: refine
Mandatory: no
Average figure of merit of phases of reflections not included in the refinement. This value is derived from the likelihood function. FOM = I_1(X)/I_0(X) I_0, I_1 = zero- and first-order modified Bessel functions of the first kind X = sigma_A |E_o| |E_c|/SIGMA E_o, E_c = normalized observed and calculated structure factors sigma_A = <cos 2 pi s delta_x> SQRT(Sigma_P/Sigma_N) estimated using maximum likelihood Sigma_P = sum_{atoms in model} f2 Sigma_N = sum_{atoms in crystal} f2 f = form factor of atoms delta_x = expected error SIGMA = (sigma_{E;exp})2 + epsilon [1-(sigma_A)2] sigma_{E;exp} = uncertainties of normalized observed structure factors epsilon = multiplicity of the diffracting plane Ref: Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997). Acta Cryst. D53, 240-255.
Alias: _refine.ebi_overall_FOM_free_Rset (ebi_extensions, 1.0)
Type: float
Category: refine
Mandatory: no
Average figure of merit of phases of reflections included in the refinement. This value is derived from the likelihood function FOM = I_1(X)/I_0(X) I_0, I_1 = zero- and first-order modified Bessel functions of the first kind X = sigma_A |E_o| |E_c|/SIGMA E_o, E_c = normalized observed and calculated structure factors sigma_A = <cos 2 pi s delta_x> SQRT(Sigma_P/Sigma_N) estimated using maximum likelihood Sigma_P = sum_{atoms in model} f2 Sigma_N = sum_{atoms in crystal} f2 f = form factor of atoms delta_x = expected error SIGMA = (sigma_{E;exp})2 + epsilon [1-(sigma_A)2] sigma_{E;exp} = uncertainties of normalized observed structure factors epsilon = multiplicity of diffracting plane Ref: Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997). Acta Cryst. D53, 240-255.
Alias: _refine.ebi_overall_FOM_work_Rset (ebi_extensions, 1.0)
Type: float
Category: refine
Mandatory: no
Special aspects of the solvent model used during refinement.
Type: text
Category: refine
Mandatory: no
The value of the BSOL solvent-model parameter describing the average isotropic displacement parameter of disordered solvent atoms. This is one of the two parameters (the other is _refine.solvent_model_param_ksol) in Tronrud's method of modelling the contribution of bulk solvent to the scattering. The standard scale factor is modified according to the expression k0 exp(-B0 * s2)[1-KSOL * exp(-BSOL * s2)] where k0 and B0 are the scale factors for the protein. Ref: Tronrud, D. E. (1997). Methods Enzymol. 277, 243-268.
Type: float
Category: refine
Mandatory: no
The value of the KSOL solvent-model parameter describing the ratio of the electron density in the bulk solvent to the electron density in the molecular solute. This is one of the two parameters (the other is _refine.solvent_model_param_bsol) in Tronrud's method of modelling the contribution of bulk solvent to the scattering. The standard scale factor is modified according to the expression k0 exp(-B0 * s2)[1-KSOL * exp(-BSOL * s2)] where k0 and B0 are the scale factors for the protein. Ref: Tronrud, D. E. (1997). Methods Enzymol. 277, 243-268.
Type: float
Data items in the REFINE_ANALYZE category record details about the refined structure that are often used to analyze the refinement and assess its quality. A given computer program may or may not produce values corresponding to these data names.
Mandatory: no
Keys: _refine_analyze.entry_id
Groups: inclusive_group refine_group
Examples:
| Example | Detail |
|---|---|
loop_
_refine_analyze.entry_id
_refine_analyze.Luzzati_coordinate_error_obs
_refine_analyze.Luzzati_d_res_low_obs
5HVP 0.056 2.51
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
Category: refine_analyze
Mandatory: yes
This data item is a pointer to _entry.id in the ENTRY category.
Category: refine_analyze
Mandatory: no
The estimated coordinate error obtained from the plot of the R value versus sin(theta)/lambda for the reflections treated as a test set during refinement. Ref: Luzzati, V. (1952). Traitement statistique des erreurs dans la determination des structures cristallines. Acta Cryst. 5, 802-810.
Type: float
Units: angstroms
Category: refine_analyze
Mandatory: no
The estimated coordinate error obtained from the plot of the R value versus sin(theta)/lambda for reflections classified as observed. Ref: Luzzati, V. (1952). Traitement statistique des erreurs dans la determination des structures cristallines. Acta Cryst. 5, 802-810.
Type: float
Units: angstroms
Category: refine_analyze
Mandatory: no
The value of the low-resolution cutoff used in constructing the Luzzati plot for reflections treated as a test set during refinement. Ref: Luzzati, V. (1952). Traitement statistique des erreurs dans la determination des structures cristallines. Acta Cryst. 5, 802-810.
Type: float
Units: angstroms
Category: refine_analyze
Mandatory: no
The value of the low-resolution cutoff used in constructing the Luzzati plot for reflections classified as observed. Ref: Luzzati, V. (1952). Traitement statistique des erreurs dans la determination des structures cristallines. Acta Cryst. 5, 802-810.
Type: float
Units: angstroms
Category: refine_analyze
Mandatory: no
The value of sigmaa used in constructing the Luzzati plot for the reflections treated as a test set during refinement. Details of the estimation of sigmaa can be specified in _refine_analyze.Luzzati_sigma_a_free_details. Ref: Luzzati, V. (1952). Traitement statistique des erreurs dans la determination des structures cristallines. Acta Cryst. 5, 802-810.
Type: float
Units: angstroms
Category: refine_analyze
Mandatory: no
Details of the estimation of sigmaa for the reflections treated as a test set during refinement. Ref: Luzzati, V. (1952). Traitement statistique des erreurs dans la determination des structures cristallines. Acta Cryst. 5, 802-810.
Type: text
Category: refine_analyze
Mandatory: no
The value of sigmaa used in constructing the Luzzati plot for reflections classified as observed. Details of the estimation of sigmaa can be specified in _refine_analyze.Luzzati_sigma_a_obs_details. Ref: Luzzati, V. (1952). Traitement statistique des erreurs dans la determination des structures cristallines. Acta Cryst. 5, 802-810.
Type: float
Units: angstroms
Category: refine_analyze
Mandatory: no
Special aspects of the estimation of sigmaa for the reflections classified as observed. Ref: Luzzati, V. (1952). Traitement statistique des erreurs dans la determination des structures cristallines. Acta Cryst. 5, 802-810.
Type: text
Category: refine_analyze
Mandatory: no
The number of discretely disordered residues in the refined model.
Type: float
Category: refine_analyze
Mandatory: no
The sum of the occupancies of the hydrogen atoms in the refined model.
Type: float
Category: refine_analyze
Mandatory: no
The sum of the occupancies of the non-hydrogen atoms in the refined model.
Type: float
Category: refine_analyze
Mandatory: no
The value of the high-resolution cutoff in angstroms used in the calculation of the Hamilton generalized R factor (RG) stored in _refine_analyze.RG_work and _refine_analyze.RG_free. Ref: Hamilton, W. C. (1965). Acta Cryst. 18, 502-510.
Alias: _refine_analyze.ebi_RG_d_res_high (ebi_extensions, 1.0)
Type: float
Units: angstroms
Range: [0.0, .] [0.0, 0.0]
Category: refine_analyze
Mandatory: no
The value of the low-resolution cutoff in angstroms used in the calculation of the Hamilton generalized R factor (RG) stored in _refine_analyze.RG_work and _refine_analyze.RG_free. Ref: Hamilton, W. C. (1965). Acta Cryst. 18, 502-510.
Alias: _refine_analyze.ebi_RG_d_res_low (ebi_extensions, 1.0)
Type: float
Units: angstroms
Range: [0.0, .] [0.0, 0.0]
Category: refine_analyze
Mandatory: no
The Hamilton generalized R factor for all reflections that satisfy the resolution limits established by _refine_analyze.RG_d_res_high and _refine_analyze.RG_d_res_low for the free R set of reflections that were excluded from the refinement. sum_i sum_j w_{i,j}(|Fobs|_i - G|Fcalc|_i)(|Fobs|_j - G|Fcalc|_j) RG = Sqrt( ----------------------------------------------------------------- ) sum_i sum_j w_{i,j} |Fobs|_i |Fobs|_j where |Fobs| = the observed structure-factor amplitudes |Fcalc| = the calculated structure-factor amplitudes G = the scale factor which puts |Fcalc| on the same scale as |Fobs| w_{i,j} = the weight for the combination of the reflections i and j. sum_i and sum_j are taken over the specified reflections When the covariance of the amplitudes of reflection i and reflection j is zero (i.e. the reflections are independent) w{i,i} can be redefined as w_i and the nested sums collapsed into one sum. sum_i w_i(|Fobs|_i - G|Fcalc|_i)2 RG = Sqrt( ----------------------------------- ) sum_i w_i |Fobs|_i2 Ref: Hamilton, W. C. (1965). Acta Cryst. 18, 502-510.
Alias: _refine_analyze.ebi_RG_free (ebi_extensions, 1.0)
Type: float
Range: [0.0, .] [0.0, 0.0]
Category: refine_analyze
Mandatory: no
The Hamilton generalized R factor for all reflections that satisfy the resolution limits established by _refine_analyze.RG_d_res_high and _refine_analyze.RG_d_res_low and for those reflections included in the working set when a free R set of reflections is omitted from the refinement. sum_i sum_j w_{i,j}(|Fobs|_i - G|Fcalc|_i)(|Fobs|_j - G|Fcalc|_j) RG = Sqrt( ----------------------------------------------------------------- ) sum_i sum_j w_{i,j} |Fobs|_i |Fobs|_j where |Fobs| = the observed structure-factor amplitudes |Fcalc| = the calculated structure-factor amplitudes G = the scale factor which puts |Fcalc| on the same scale as |Fobs| w_{i,j} = the weight for the combination of the reflections i and j. sum_i and sum_j are taken over the specified reflections When the covariance of the amplitudes of reflection i and reflection j is zero (i.e. the reflections are independent) w{i,i} can be redefined as w_i and the nested sums collapsed into one sum. sum_i w_i(|Fobs|_i - G|Fcalc|_i)2 RG = Sqrt( ----------------------------------- ) sum_i w_i |Fobs|_i2 Ref: Hamilton, W. C. (1965). Acta Cryst. 18, 502-510.
Alias: _refine_analyze.ebi_RG_work (ebi_extensions, 1.0)
Type: float
Range: [0.0, .] [0.0, 0.0]
Category: refine_analyze
Mandatory: no
The observed ratio of RGfree to RGwork. The expected RG ratio is the value that should be achievable at the end of a structure refinement when only random uncorrelated errors exist in the data and the model provided that the observations are properly weighted. When compared with the observed RG ratio it may indicate that a structure has not reached convergence or a model has been over-refined with no corresponding improvement in the model. In an unrestrained refinement, the ratio of RGfree to RGwork with only random uncorrelated errors at convergence depends only on the number of reflections and the number of parameters according to sqrt[(f + m) / (f - m) ] where f = the number of included structure amplitudes and target distances, and m = the number of parameters being refined. In the restrained case, RGfree is calculated from a random selection of residuals including both structure amplitudes and restraints. When restraints are included in the refinement, the RG ratio requires a term for the contribution to the minimized residual at convergence, Drestr, due to those restraints: Drestr = r - sum [w_i . (a_i)t . (H)-1 a_i] where r is the number of geometrical, displacement-parameter and other restraints H is the (m,m) normal matrix given by A^t.W.A W is the (n,n) symmetric weight matrix of the included observations A is the least-squares design matrix of derivatives of order (n,m) a_i is the ith row of A Then the expected RGratio becomes sqrt [ (f + (m - r + Drestr))/ (f - (m - r + Drestr)) ] There is no data name for the expected value of RGfree/RGwork yet. Ref: Tickle, I. J., Laskowski, R. A. & Moss, D. S. (1998). Acta Cryst. D54, 547-557.
Alias: _refine_analyze.ebi_RG_work_free_ratio (ebi_extensions, 1.0)
Type: float
Range: [0.0, .] [0.0, 0.0]
Data items in the REFINE_B_ISO category record details about the treatment of isotropic B factors (displacement parameters) during refinement.
Mandatory: no
Keys: _refine_B_iso.class
Groups: inclusive_group refine_group
Examples:
| Example | Detail |
|---|---|
loop_
_refine_B_iso.class
_refine_B_iso.treatment
'protein' isotropic
'solvent' isotropic
'inhibitor' isotropic
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
Category: refine_B_iso
Mandatory: yes
A class of atoms treated similarly for isotropic B-factor (displacement-parameter) refinement.
Type: text
Examples:
| Example | Detail |
|---|---|
all |
|
protein |
|
solvent |
|
sugar-phosphate backbone |
Category: refine_B_iso
Mandatory: no
A description of special aspects of the isotropic B-factor (displacement-parameter) refinement for the class of atoms described in _refine_B_iso.class.
Type: text
Example:
The temperature factors of atoms in the side
chain of Arg 92 were held fixed due to
unstable behavior in refinement.
Category: refine_B_iso
Mandatory: no
The treatment of isotropic B-factor (displacement-parameter) refinement for a class of atoms defined in _refine_B_iso.class.
Type: ucode
Enumeration values:
| Value | Detail |
|---|---|
fixed |
|
isotropic |
|
anisotropic |
Category: refine_B_iso
Mandatory: no
The value of the isotropic B factor (displacement parameter) assigned to a class of atoms defined in _refine_B_iso.class. Meaningful only for atoms with fixed isotropic B factors.
Type: float
Units: angstroms_squared
Data items in the REFINE_FUNCT_MINIMIZED category record details about the individual terms of the function minimized during refinement.
Mandatory: no
Keys: _refine_funct_minimized.type
Groups: inclusive_group refine_group
Examples:
| Example | Detail |
|---|---|
loop_
_refine_funct_minimized.type
_refine_funct_minimized.number_terms
_refine_funct_minimized.residual
'sum(W*Delta(Amplitude)^2' 3009 1621.3
'sum(W*Delta(Plane+Rigid)^2' 85 56.68
'sum(W*Delta(Distance)^2' 1219 163.59
'sum(W*Delta(U-tempfactors)^2' 1192 69.338
|
Example 1 - based on RESTRAIN refinement for the CCP4 test data set toxd. |
Category: refine_funct_minimized
Mandatory: no
The number of observations in this term. For example, if the term is a residual of the X-ray intensities, this item would contain the number of reflections used in the refinement.
Alias: _ebi_refine_funct_minimized.NumTerms (ebi_extensions, 1.0)
Type: int
Range: [0, .] [0, 0]
Category: refine_funct_minimized
Mandatory: no
The residual for this term of the function that was minimized during the refinement.
Alias: _ebi_refine_funct_minimized.Residual (ebi_extensions, 1.0)
Type: float
Range: [0.0, .] [0.0, 0.0]
Category: refine_funct_minimized
Mandatory: yes
The type of the function being minimized.
Alias: _ebi_refine_funct_minimized.type (ebi_extensions, 1.0)
Type: line
Category: refine_funct_minimized
Mandatory: no
The weight applied to this term of the function that was minimized during the refinement.
Alias: _ebi_refine_funct_minimized.weight (ebi_extensions, 1.0)
Type: float
Data items in the REFINE_HIST category record details about the steps during the refinement of the structure. These data items are not meant to be as thorough a description of the refinement as is provided for the final model in other categories; rather, these data items provide a mechanism for sketching out the progress of the refinement, supported by a small set of representative statistics.
Mandatory: no
Keys: _refine_hist.cycle_id
Groups: inclusive_group refine_group
Examples:
| Example | Detail |
|---|---|
_refine_hist.cycle_id C134
_refine_hist.d_res_high 1.85
_refine_hist.d_res_low 20.0
_refine_hist.number_atoms_solvent 217
_refine_hist.number_atoms_total 808
_refine_hist.number_reflns_all 6174
_refine_hist.number_reflns_obs 4886
_refine_hist.number_reflns_R_free 476
_refine_hist.number_reflns_R_work 4410
_refine_hist.R_factor_all .265
_refine_hist.R_factor_obs .195
_refine_hist.R_factor_R_free .274
_refine_hist.R_factor_R_work .160
_refine_hist.details
; Add majority of solvent molecules. B factors refined by
group. Continued to remove misplaced water molecules.
;
|
Example 1 - based on laboratory records for the collagen-like peptide [(POG)4 EKG (POG)5]3. |
Category: refine_hist
Mandatory: yes
The value of _refine_hist.cycle_id must uniquely identify a record in the REFINE_HIST list. Note that this item need not be a number; it can be any unique identifier.
Type: code
Category: refine_hist
Mandatory: no
A description of special aspects of this cycle of the refinement process.
Type: text
Example:
Residues 13-17 fit and added to model;
substantial rebuilding of loop containing
residues 43-48; addition of first atoms to
solvent model; ten cycles of Prolsq
refinement.
Category: refine_hist
Mandatory: yes
The lowest value for the interplanar spacings for the reflection data for this cycle of refinement. This is called the highest resolution.
Type: float
Units: angstroms
Range: [0.0, .] [0.0, 0.0]
Category: refine_hist
Mandatory: yes
The highest value for the interplanar spacings for the reflection data for this cycle of refinement. This is called the lowest resolution.
Type: float
Units: angstroms
Range: [0.0, .] [0.0, 0.0]
Category: refine_hist
Mandatory: no
The number of solvent atoms that were included in the model at this cycle of the refinement.
Type: int
Range: [0, .] [0, 0]
Category: refine_hist
Mandatory: no
The total number of atoms that were included in the model at this cycle of the refinement.
Type: int
Range: [0, .] [0, 0]
Category: refine_hist
Mandatory: no
The number of reflections that satisfy the resolution limits established by _refine_hist.d_res_high and _refine_hist.d_res_low.
Type: int
Range: [0, .] [0, 0]
Category: refine_hist
Mandatory: no
The number of reflections that satisfy the resolution limits established by _refine_hist.d_res_high and _refine_hist.d_res_low and the observation criterion established by _reflns.observed_criterion.
Type: int
Range: [0, .] [0, 0]
Category: refine_hist
Mandatory: no
The number of reflections that satisfy the resolution limits established by _refine_hist.d_res_high and _refine_hist.d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details.
Type: int
Range: [0, .] [0, 0]
Category: refine_hist
Mandatory: no
The number of reflections that satisfy the resolution limits established by _refine_hist.d_res_high and _refine_hist.d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the working reflections (i.e. were included in the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details.
Type: int
Range: [0, .] [0, 0]
Category: refine_hist
Mandatory: no
Residual factor R for reflections that satisfy the resolution limits established by _refine_hist.d_res_high and _refine_hist.d_res_low. sum|Fobs - Fcalc| R = --------------------- sum|Fobs| Fobs = the observed structure-factor amplitudes Fcalc = the calculated structure-factor amplitudes sum is taken over the specified reflections
Type: float
Range: [0.0, .] [0.0, 0.0]
Category: refine_hist
Mandatory: no
Residual factor R for reflections that satisfy the resolution limits established by _refine_hist.d_res_high and _refine_hist.d_res_low and the observation criterion established by _reflns.observed_criterion. sum|Fobs - Fcalc| R = --------------------- sum|Fobs| Fobs = the observed structure-factor amplitudes Fcalc = the calculated structure-factor amplitudes sum is taken over the specified reflections
Type: float
Range: [0.0, .] [0.0, 0.0]
Category: refine_hist
Mandatory: no
Residual factor R for reflections that satisfy the resolution limits established by _refine_hist.d_res_high and _refine_hist.d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details. sum|Fobs - Fcalc| R = --------------------- sum|Fobs| Fobs = the observed structure-factor amplitudes Fcalc = the calculated structure-factor amplitudes sum is taken over the specified reflections
Type: float
Range: [0.0, .] [0.0, 0.0]
Category: refine_hist
Mandatory: no
Residual factor R for reflections that satisfy the resolution limits established by _refine_hist.d_res_high and _refine_hist.d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the working reflections (i.e. were included in the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details. sum|Fobs - Fcalc| R = --------------------- sum|Fobs| Fobs = the observed structure-factor amplitudes Fcalc = the calculated structure-factor amplitudes sum is taken over the specified reflections
Type: float
Range: [0.0, .] [0.0, 0.0]
Data items in the REFINE_LS_RESTR category record details about the restraints applied to various classes of parameters during the least-squares refinement.
Mandatory: no
Keys: _refine_ls_restr.type
Groups: inclusive_group refine_group
Examples:
| Example | Detail |
|---|---|
loop_
_refine_ls_restr.type
_refine_ls_restr.dev_ideal_target
_refine_ls_restr.dev_ideal
_refine_ls_restr.number
_refine_ls_restr.criterion
_refine_ls_restr.rejects
'bond_d' 0.020 0.018 1654 '> 2\s' 22
'angle_d' 0.030 0.038 2246 '> 2\s' 139
'planar_d' 0.040 0.043 498 '> 2\s' 21
'planar' 0.020 0.015 270 '> 2\s' 1
'chiral' 0.150 0.177 278 '> 2\s' 2
'singtor_nbd' 0.500 0.216 582 '> 2\s' 0
'multtor_nbd' 0.500 0.207 419 '> 2\s' 0
'xyhbond_nbd' 0.500 0.245 149 '> 2\s' 0
'planar_tor' 3.0 2.6 203 '> 2\s' 9
'staggered_tor' 15.0 17.4 298 '> 2\s' 31
'orthonormal_tor' 20.0 18.1 12 '> 2\s' 1
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
Category: refine_ls_restr
Mandatory: no
A criterion used to define a parameter value that deviates significantly from its ideal value in the model obtained by restrained least-squares refinement.
Type: text
Example:
> 3\s
Category: refine_ls_restr
Mandatory: no
For the given parameter type, the root-mean-square deviation between the ideal values used as restraints in the least-squares refinement and the values obtained by refinement. For instance, bond distances may deviate by 0.018 Å (r.m.s.) from ideal values in the current model.
Type: float
Range: [0.0, .] [0.0, 0.0]
Category: refine_ls_restr
Mandatory: no
For the given parameter type, the target root-mean-square deviation between the ideal values used as restraints in the least-squares refinement and the values obtained by refinement.
Type: float
Range: [0.0, .] [0.0, 0.0]
Category: refine_ls_restr
Mandatory: no
The number of parameters of this type subjected to restraint in least-squares refinement.
Type: int
Range: [0, .] [0, 0]
Category: refine_ls_restr
Mandatory: no
The number of parameters of this type that deviate from ideal values by more than the amount defined in _refine_ls_restr.criterion in the model obtained by restrained least-squares refinement.
Type: int
Range: [0, .] [0, 0]
| Name | Category | Mandatory |
|---|---|---|
| _refine_ls_restr.type | refine_ls_restr | yes |
| _refine_ls_restr_type.type | refine_ls_restr_type | yes |
The type of the parameter being restrained. Explicit sets of data values are provided for the programs PROTIN/PROLSQ (beginning with p_) and RESTRAIN (beginning with RESTRAIN_). As computer programs change, these data values are given as examples, not as an enumeration list. Computer programs that convert a data block to a refinement table will expect the exact form of the data values given here to be used.
Type: line
Child / Parent relations:
| Child | Parent |
|---|---|
| _refine_ls_restr_type.type | _refine_ls_restr.type |
Examples:
| Example | Detail |
|---|---|
p_bond_d |
bond distance |
p_angle_d |
bond angle expressed as a distance |
p_planar_d |
planar 1,4 distance |
p_xhbond_d |
X-H bond distance |
p_xhangle_d |
X-H bond angle expressed as a distance |
p_hydrog_d |
hydrogen distance |
p_special_d |
special distance |
p_planar |
planes |
p_chiral |
chiral centres |
p_singtor_nbd |
single-torsion non-bonded contact |
p_multtor_nbd |
multiple-torsion non-bonded contact |
p_xyhbond_nbd |
possible (X...Y) hydrogen bond |
p_xhyhbond_nbd |
possible (X-H...Y) hydrogen bond |
p_special_tor |
special torsion angle |
p_planar_tor |
planar torsion angle |
p_staggered_tor |
staggered torsion angle |
p_orthonormal_tor |
orthonormal torsion angle |
p_mcbond_it |
main-chain bond isotropic displacement parameter |
p_mcangle_it |
main-chain angle isotropic displacement parameter |
p_scbond_it |
side-chain bond isotropic displacement parameter |
p_scangle_it |
side-chain angle isotropic displacement parameter |
p_xhbond_it |
X-H bond isotropic displacement parameter |
p_xhangle_it |
X-H angle isotropic displacement parameter |
p_special_it |
special isotropic displacement parameter |
RESTRAIN_Distances < 2.12 |
The root-mean-square deviation of the difference between the values calculated from the structures used to compile the restraints dictionary parameters and the dictionary values themselves in the distance range less than 2.12 Angstroms. |
RESTRAIN_Distances 2.12 < D < 2.625 |
The root-mean-square deviation of the difference between the values calculated from the structures used to compile the restraints dictionary parameters and the dictionary values themselves in the distance range 2.12 - 2.625 Angstroms. |
RESTRAIN_Distances > 2.625 |
The root-mean-square deviation of the difference between the values calculated from the structures used to compile the restraints dictionary parameters and the dictionary values themselves in the distance range greater than 2.625 Angstroms. |
RESTRAIN_Peptide Planes |
The root-mean-square deviation of the difference between the values calculated from the structures used to compile the restraints dictionary parameters and the dictionary values themselves for peptide planes. |
RESTRAIN_Ring and other planes |
The root-mean-square deviation of the difference between the values calculated from the structures used to compile the restraints dictionary parameters and the dictionary values themselves for rings and planes other than peptide planes. |
RESTRAIN_rms diffs for Uiso atoms at dist 1.2-1.4 |
. |
RESTRAIN_rms diffs for Uiso atoms at dist 1.4-1.6 |
. |
RESTRAIN_rms diffs for Uiso atoms at dist 1.8-2.0 |
. |
RESTRAIN_rms diffs for Uiso atoms at dist 2.0-2.2 |
. |
RESTRAIN_rms diffs for Uiso atoms at dist 2.2-2.4 |
. |
RESTRAIN_rms diffs for Uiso atoms at dist >2.4 |
. |
Category: refine_ls_restr
Mandatory: no
The weighting value applied to this type of restraint in the least-squares refinement.
Type: float
Data items in the REFINE_LS_RESTR_NCS category record details about the restraints applied to atom positions in domains related by noncrystallographic symmetry during least-squares refinement, and also about the deviation of the restrained atomic parameters at the end of the refinement. It is expected that these values will only be reported once for each set of restrained domains.
Mandatory: no
Keys: _refine_ls_restr_ncs.dom_id
Groups: inclusive_group refine_group
Examples:
| Example | Detail |
|---|---|
_refine_ls_restr_ncs.dom_id d2
_refine_ls_restr_ncs.weight_position 300.0
_refine_ls_restr_ncs.weight_B_iso 2.0
_refine_ls_restr_ncs.rms_dev_position 0.09
_refine_ls_restr_ncs.rms_dev_B_iso 0.16
_refine_ls_restr_ncs.ncs_model_details
;
NCS restraint for pseudo-twofold symmetry between domains
d1 and d2. Position weight coefficient given in
Kcal/(mol \%A^2^) and isotropic B weight coefficient given
in \%A^2^.
;
|
Example 1 - based on laboratory records for the collagen-like peptide, HYP-. |
Category: refine_ls_restr_ncs
Mandatory: yes
This data item is a pointer to _struct_ncs_dom.id in the STRUCT_NCS_DOM category.
Type: code
Category: refine_ls_restr_ncs
Mandatory: no
Special aspects of the manner in which noncrystallographic restraints were applied to atomic parameters in the domain specified by _refine_ls_restr_ncs.dom_id and equivalent atomic parameters in the domains against which it was restrained.
Type: text
Category: refine_ls_restr_ncs
Mandatory: no
The root-mean-square deviation in equivalent isotropic displacement parameters in the domain specified by _refine_ls_restr_ncs.dom_id and in the domains against which it was restrained.
Type: float
Units: angstroms_squared
Range: [0.0, .] [0.0, 0.0]
Category: refine_ls_restr_ncs
Mandatory: no
The root-mean-square deviation in equivalent atom positions in the domain specified by _refine_ls_restr_ncs.dom_id and in the domains against which it was restrained.
Type: float
Units: angstroms
Range: [0.0, .] [0.0, 0.0]
Category: refine_ls_restr_ncs
Mandatory: no
The value of the weighting coefficient used in noncrystallographic symmetry restraint of isotropic displacement parameters in the domain specified by _refine_ls_restr_ncs.dom_id to equivalent isotropic displacement parameters in the domains against which it was restrained.
Type: float
Category: refine_ls_restr_ncs
Mandatory: no
The value of the weighting coefficient used in noncrystallographic symmetry restraint of atom positions in the domain specified by _refine_ls_restr_ncs.dom_id to equivalent atom positions in the domains against which it was restrained.
Type: float
Data items in the REFINE_LS_RESTR_TYPE category record details about the restraint types used in the least-squares refinement.
Mandatory: no
Keys: _refine_ls_restr_type.type
Groups: inclusive_group refine_group
Examples:
| Example | Detail |
|---|---|
loop_
_refine_ls_restr.type
_refine_ls_restr.number
_refine_ls_restr.dev_ideal
_refine_ls_restr.dev_ideal_target
'RESTRAIN_Distances < 2.12' 509 0.005 0.022
'RESTRAIN_Distances 2.12 < D < 2.625' 671 0.016 0.037
'RESTRAIN_Distances > 2.625' 39 0.034 0.043
'RESTRAIN_Peptide Planes' 59 0.002 0.010
'RESTRAIN_Ring and other planes' 26 0.014 0.010
'RESTRAIN_rms diffs for Uiso atoms at dist 1.2-1.4'
212 0.106 .
'RESTRAIN_rms diffs for Uiso atoms at dist 1.4-1.6'
288 0.101 .
'RESTRAIN_rms diffs for Uiso atoms at dist 1.8-2.0'
6 0.077 .
'RESTRAIN_rms diffs for Uiso atoms at dist 2.0-2.2'
10 0.114 .
'RESTRAIN_rms diffs for Uiso atoms at dist 2.2-2.4'
215 0.119 .
'RESTRAIN_rms diffs for Uiso atoms at dist >2.4'
461 0.106 .
loop_
_refine_ls_restr_type.type
_refine_ls_restr_type.distance_cutoff_low
_refine_ls_restr_type.distance_cutoff_high
'RESTRAIN_Distances < 2.12' . 2.12
'RESTRAIN_Distances 2.12 < D < 2.625' 2.12 2.625
'RESTRAIN_Distances > 2.625' 2.625 .
'RESTRAIN_Peptide Planes' . .
'RESTRAIN_Ring and other planes' . .
'RESTRAIN_rms diffs for Uiso atoms at dist 1.2-1.4'
1.2 1.4
'RESTRAIN_rms diffs for Uiso atoms at dist 1.4-1.6'
1.4 1.6
'RESTRAIN_rms diffs for Uiso atoms at dist 1.8-2.0'
1.8 2.0
'RESTRAIN_rms diffs for Uiso atoms at dist 2.0-2.2'
2.0 2.2
'RESTRAIN_rms diffs for Uiso atoms at dist 2.2-2.4'
2.2 2.4
'RESTRAIN_rms diffs for Uiso atoms at dist >2.4'
2.4 .
|
Example 1 - based on RESTRAIN refinement for the CCP4 test data set toxd. |
Category: refine_ls_restr_type
Mandatory: no
The upper limit in angstroms of the distance range applied to the current restraint type.
Type: float
Units: angstroms
Range: [0.0, .] [0.0, 0.0]
Category: refine_ls_restr_type
Mandatory: no
The lower limit in angstroms of the distance range applied to the current restraint type.
Type: float
Units: angstroms
Range: [0.0, .] [0.0, 0.0]
Category: refine_ls_restr_type
Mandatory: yes
This data item is a pointer to _refine_ls_restr.type in the REFINE_LS_RESTR category.
Type: line
Data items in the REFINE_LS_SHELL category record details about the results of the least-squares refinement broken down into shells of resolution.
Mandatory: no
Keys: _refine_ls_shell.d_res_low _refine_ls_shell.d_res_high
Groups: inclusive_group refine_group
Examples:
| Example | Detail |
|---|---|
loop_
_refine_ls_shell.d_res_low
_refine_ls_shell.d_res_high
_refine_ls_shell.number_reflns_obs
_refine_ls_shell.R_factor_obs
8.00 4.51 1226 0.196
4.51 3.48 1679 0.146
3.48 2.94 2014 0.160
2.94 2.59 2147 0.182
2.59 2.34 2127 0.193
2.34 2.15 2061 0.203
2.15 2.00 1647 0.188
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
Category: refine_ls_shell
Mandatory: yes
The lowest value for the interplanar spacings for the reflection data in this shell. This is called the highest resolution.
Type: float
Units: angstroms
Range: [0.0, .] [0.0, 0.0]
Category: refine_ls_shell
Mandatory: yes
The highest value for the interplanar spacings for the reflection data in this shell. This is called the lowest resolution.
Type: float
Units: angstroms
Range: [0.0, .] [0.0, 0.0]
Category: refine_ls_shell
Mandatory: no
The number of reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low.
Type: int
Range: [0, .] [0, 0]
Category: refine_ls_shell
Mandatory: no
The number of reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation criterion established by _reflns.observed_criterion.
Type: int
Range: [0, .] [0, 0]
Category: refine_ls_shell
Mandatory: no
The number of reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details.
Type: int
Range: [0, .] [0, 0]
Category: refine_ls_shell
Mandatory: no
The number of reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the working reflections (i.e. were included in the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details.
Type: int
Range: [0, .] [0, 0]
Category: refine_ls_shell
Mandatory: no
The number of reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation criterion established by _reflns.observed_criterion, expressed as a percentage of the number of geometrically observable reflections that satisfy the resolution limits.
Type: float
Category: refine_ls_shell
Mandatory: no
The number of reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor, expressed as a percentage of the number of geometrically observable reflections that satisfy the reflection limits.
Type: float
Category: refine_ls_shell
Mandatory: no
Residual factor R for reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low. sum|Fobs - Fcalc| R = --------------------- sum|Fobs| Fobs = the observed structure-factor amplitudes Fcalc = the calculated structure-factor amplitudes sum is taken over the specified reflections
Type: float
Related item: _refine_ls_shell.wR_factor_all (alternate)
Range: [0.0, .] [0.0, 0.0]
Category: refine_ls_shell
Mandatory: no
Residual factor R for reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation criterion established by _reflns.observed_criterion. sum|Fobs - Fcalc| R = --------------------- sum|Fobs| Fobs = the observed structure-factor amplitudes Fcalc = the calculated structure-factor amplitudes sum is taken over the specified reflections
Type: float
Related item: _refine_ls_shell.wR_factor_obs (alternate)
Range: [0.0, .] [0.0, 0.0]
Category: refine_ls_shell
Mandatory: no
Residual factor R for reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details. sum|Fobs - Fcalc| R = --------------------- sum|Fobs| Fobs = the observed structure-factor amplitudes Fcalc = the calculated structure-factor amplitudes sum is taken over the specified reflections
Type: float
Related items: _refine_ls_shell.wR_factor_R_free (alternate) _refine_ls_shell.R_factor_R_free_error (associated_error)
Range: [0.0, .] [0.0, 0.0]
Category: refine_ls_shell
Mandatory: no
The estimated error in _refine_ls_shell.R_factor_R_free. The method used to estimate the error is described in the item _refine.ls_R_factor_R_free_error_details.
Type: float
Related item: _refine_ls_shell.R_factor_R_free (associated_value)
Category: refine_ls_shell
Mandatory: no
Residual factor R for reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the working reflections (i.e. were included in the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details. sum|Fobs - Fcalc| R = --------------------- sum|Fobs| Fobs = the observed structure-factor amplitudes Fcalc = the calculated structure-factor amplitudes sum is taken over the specified reflections
Type: float
Related item: _refine_ls_shell.wR_factor_R_work (alternate)
Range: [0.0, .] [0.0, 0.0]
Category: refine_ls_shell
Mandatory: no
The ratio of the total number of observations of the reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low to the number of crystallographically unique reflections that satisfy the same limits.
Type: float
Category: refine_ls_shell
Mandatory: no
The ratio of the total number of observations of the reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation criterion established by _reflns.observed_criterion to the number of crystallographically unique reflections that satisfy the same limits.
Type: float
Category: refine_ls_shell
Mandatory: no
Weighted residual factor wR for reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low. ( sum|w |Yobs - Ycalc|2| )1/2 wR = ( ---------------------------- ) ( sum|w Yobs2| ) Yobs = the observed amplitude specified by _refine.ls_structure_factor_coef Ycalc = the calculated amplitude specified by _refine.ls_structure_factor_coef w = the least-squares weight sum is taken over the specified reflections
Type: float
Related item: _refine_ls_shell.R_factor_all (alternate)
Range: [0.0, .] [0.0, 0.0]
Category: refine_ls_shell
Mandatory: no
Weighted residual factor wR for reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation criterion established by _reflns.observed_criterion. ( sum|w |Yobs - Ycalc|2| )1/2 wR = ( ---------------------------- ) ( sum|w Yobs2| ) Yobs = the observed amplitude specified by _refine.ls_structure_factor_coef Ycalc = the calculated amplitude specified by _refine.ls_structure_factor_coef w = the least-squares weight sum is taken over the specified reflections
Type: float
Related item: _refine_ls_shell.R_factor_obs (alternate)
Range: [0.0, .] [0.0, 0.0]
Category: refine_ls_shell
Mandatory: no
Weighted residual factor wR for reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details. ( sum|w |Yobs - Ycalc|2| )1/2 wR = ( ---------------------------- ) ( sum|w Yobs2| ) Yobs = the observed amplitude specified by _refine.ls_structure_factor_coef Ycalc = the calculated amplitude specified by _refine.ls_structure_factor_coef w = the least-squares weight sum is taken over the specified reflections
Type: float
Related item: _refine_ls_shell.R_factor_R_free (alternate)
Range: [0.0, .] [0.0, 0.0]
Category: refine_ls_shell
Mandatory: no
Weighted residual factor wR for reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the working reflections (i.e. were included in the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details. ( sum|w |Yobs - Ycalc|2| )1/2 wR = ( ---------------------------- ) ( sum|w Yobs2| ) Yobs = the observed amplitude specified by _refine.ls_structure_factor_coef Ycalc = the calculated amplitude specified by _refine.ls_structure_factor_coef w = the least-squares weight sum is taken over the specified reflections
Type: float
Related item: _refine_ls_shell.R_factor_R_work (alternate)
Range: [0.0, .] [0.0, 0.0]
Data items in the REFINE_OCCUPANCY category record details about the treatment of atom occupancies during refinement.
Mandatory: no
Keys: _refine_occupancy.class
Groups: inclusive_group refine_group
Examples:
| Example | Detail |
|---|---|
loop_
_refine_occupancy.class
_refine_occupancy.treatment
_refine_occupancy.value
_refine_occupancy.details
'protein' fix 1.00 .
'solvent' fix 1.00 .
'inhibitor orientation 1' fix 0.65 .
'inhibitor orientation 2' fix 0.35
; The inhibitor binds to the enzyme in two alternative
conformations. The occupancy of each conformation was
adjusted so as to result in approximately equal mean
thermal factors for the atoms in each conformation.
;
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
Category: refine_occupancy
Mandatory: yes
The class of atoms treated similarly for occupancy refinement.
Type: text
Examples:
| Example | Detail |
|---|---|
all |
|
protein |
|
solvent |
|
sugar-phosphate backbone |
Category: refine_occupancy
Mandatory: no
A description of special aspects of the occupancy refinement for a class of atoms described in _refine_occupancy.class.
Type: text
Example:
The inhibitor binds to the enzyme in two
alternative conformations. The occupancy of
each conformation was adjusted so as to result
in approximately equal mean thermal factors
for the atoms in each conformation.
Category: refine_occupancy
Mandatory: no
The treatment of occupancies for a class of atoms described in _refine_occupancy.class.
Type: ucode
Enumeration values:
| Value | Detail |
|---|---|
fix |
fixed |
ref |
refined |
Category: refine_occupancy
Mandatory: no
The value of occupancy assigned to a class of atoms defined in _refine_occupancy.class. Meaningful only for atoms with fixed occupancy.
Type: float
Range: [1.0, 1.0] [0.0, 1.0] [0.0, 0.0]
Examples:
| Example | Detail |
|---|---|
1.0 |
|
0.41 |
Data items in the REFLN category record details about the reflection data used to determine the ATOM_SITE data items. The REFLN data items refer to individual reflections and must be included in looped lists. The REFLNS data items specify the parameters that apply to all reflections. The REFLNS data items are not looped.
Mandatory: no
Keys: _refln.index_h _refln.index_k _refln.index_l
Groups: inclusive_group refln_group
Examples:
| Example | Detail |
|---|---|
loop_
_refln.index_h
_refln.index_k
_refln.index_l
_refln.F_squared_calc
_refln.F_squared_meas
_refln.F_squared_sigma
_refln.status
2 0 0 85.57 58.90 1.45 o
3 0 0 15718.18 15631.06 30.40 o
4 0 0 55613.11 49840.09 61.86 o
5 0 0 246.85 241.86 10.02 o
6 0 0 82.16 69.97 1.93 o
7 0 0 1133.62 947.79 11.78 o
8 0 0 2558.04 2453.33 20.44 o
9 0 0 283.88 393.66 7.79 o
10 0 0 283.70 171.98 4.26 o
|
Example 1 - based on data set fetod of Todres, Yanovsky, Ermekov & Struchkov [Acta Cryst. (1993), C49, 1352-1354]. |
Category: refln
Mandatory: no
The calculated value of structure-factor component A in electrons. A = |F|cos(phase)
Alias: _refln_A_calc (cif_core.dic, 2.0.1)
Type: float
Units: electrons
Related item: _refln.A_calc_au (conversion_arbitrary)
Category: refln
Mandatory: no
The calculated value of structure-factor component A in arbitrary units. A = |F|cos(phase)
Type: float
Units: arbitrary
Related item: _refln.A_calc (conversion_arbitrary)
Category: refln
Mandatory: no
The measured value of structure-factor component A in electrons. A = |F|cos(phase)
Alias: _refln_A_meas (cif_core.dic, 2.0.1)
Type: float
Units: electrons
Related item: _refln.A_meas_au (conversion_arbitrary)
Category: refln
Mandatory: no
The measured value of structure-factor component A in arbitrary units. A = |F|cos(phase)
Type: float
Units: arbitrary
Related item: _refln.A_meas (conversion_arbitrary)
Category: refln
Mandatory: no
The calculated value of structure-factor component B in electrons. B = |F|sin(phase)
Alias: _refln_B_calc (cif_core.dic, 2.0.1)
Type: float
Units: electrons
Related item: _refln.B_calc_au (conversion_arbitrary)
Category: refln
Mandatory: no
The calculated value of structure-factor component B in arbitrary units. B = |F|sin(phase)
Type: float
Units: arbitrary
Related item: _refln.B_calc (conversion_arbitrary)
Category: refln
Mandatory: no
The measured value of structure-factor component B in electrons. B = |F|sin(phase)
Alias: _refln_B_meas (cif_core.dic, 2.0.1)
Type: float
Units: electrons
Related item: _refln.B_meas_au (conversion_arbitrary)
Category: refln
Mandatory: no
The measured value of structure-factor component B in arbitrary units. B = |F|sin(phase)
Type: float
Units: arbitrary
Related item: _refln.B_meas (conversion_arbitrary)
Mandatory: yes
This data item is a pointer to _exptl_crystal.id in the EXPTL_CRYSTAL category.
Alias: _refln_crystal_id (cif_core.dic, 2.0.1)
Category: refln
Mandatory: no
The calculated value of the structure factor in electrons.
Alias: _refln_F_calc (cif_core.dic, 2.0.1)
Type: float
Units: electrons
Related item: _refln.F_calc_au (conversion_arbitrary)
Category: refln
Mandatory: no
The calculated value of the structure factor in arbitrary units.
Type: float
Units: arbitrary
Related item: _refln.F_calc (conversion_arbitrary)
Category: refln
Mandatory: no
The measured value of the structure factor in electrons.
Alias: _refln_F_meas (cif_core.dic, 2.0.1)
Type: float
Type conditions: esd
Units: electrons
Related items: _refln.F_meas_sigma (associated_esd) _refln.F_meas_au (conversion_arbitrary)
Category: refln
Mandatory: no
The measured value of the structure factor in arbitrary units.
Type: float
Type conditions: esd
Units: arbitrary
Related items: _refln.F_meas_sigma_au (associated_esd) _refln.F_meas (conversion_arbitrary)
Category: refln
Mandatory: no
The standard uncertainty (estimated standard deviation) of _refln.F_meas in electrons.
Alias: _refln_F_sigma (cif_core.dic, 2.0.1)
Type: float
Units: electrons
Related items: _refln.F_meas (associated_value) _refln.F_meas_sigma_au (conversion_arbitrary)
Category: refln
Mandatory: no
The standard uncertainty (estimated standard deviation) of _refln.F_meas_au in arbitrary units.
Type: float
Units: arbitrary
Related items: _refln.F_meas_au (associated_value) _refln.F_meas_sigma (conversion_arbitrary)
Category: refln
Mandatory: no
The calculated value of the squared structure factor in electrons squared.
Alias: _refln_F_squared_calc (cif_core.dic, 2.0.1)
Type: float
Units: electrons_squared
Category: refln
Mandatory: no
The measured value of the squared structure factor in electrons squared.
Alias: _refln_F_squared_meas (cif_core.dic, 2.0.1)
Type: float
Units: electrons_squared
Category: refln
Mandatory: no
The standard uncertainty (derived from measurement) of the squared structure factor in electrons squared.
Alias: _refln_F_squared_sigma (cif_core.dic, 2.0.1)
Type: float
Units: electrons_squared
Category: refln
Mandatory: no
The figure of merit m for this reflection. int Palpha exp(i*alpha) dalpha m = -------------------------------- int Palpha dalpha Pa = the probability that the phase angle a is correct int is taken over the range alpha = 0 to 2 pi.
Type: float
Range: [0.0, .] [0.0, 0.0]
Category: refln
Mandatory: yes
Sub-category: miller_index
Miller index h of the reflection. The values of the Miller indices in the REFLN category must correspond to the cell defined by cell lengths and cell angles in the CELL category.
Alias: _refln_index_h (cif_core.dic, 2.0.1)
Type: int
Dependent items: _refln.index_k _refln.index_l
Category: refln
Mandatory: yes
Sub-category: miller_index
Miller index k of the reflection. The values of the Miller indices in the REFLN category must correspond to the cell defined by cell lengths and cell angles in the CELL category.
Alias: _refln_index_k (cif_core.dic, 2.0.1)
Type: int
Dependent items: _refln.index_h _refln.index_l
Category: refln
Mandatory: yes
Sub-category: miller_index
Miller index l of the reflection. The values of the Miller indices in the REFLN category must correspond to the cell defined by cell lengths and cell angles in the CELL category.
Alias: _refln_index_l (cif_core.dic, 2.0.1)
Type: int
Dependent items: _refln.index_h _refln.index_k
Category: refln
Mandatory: no
The calculated value of the intensity in the same units as _refln.intensity_meas.
Alias: _refln_intensity_calc (cif_core.dic, 2.0.1)
Type: float
Category: refln
Mandatory: no
The measured value of the intensity.
Alias: _refln_intensity_meas (cif_core.dic, 2.0.1)
Type: float
Category: refln
Mandatory: no
The standard uncertainty (derived from measurement) of the intensity in the same units as _refln.intensity_meas.
Alias: _refln_intensity_sigma (cif_core.dic, 2.0.1)
Type: float
Category: refln
Mandatory: no
Classification of a reflection so as to indicate its status with respect to inclusion in the refinement and the calculation of R factors.
Alias: _refln_observed_status (cif_core.dic, 2.0.1)
Type: ucode
Enumeration values:
| Value | Detail |
|---|---|
o |
satisfies _refine.ls_d_res_high, satisfies _refine.ls_d_res_low, observed by _reflns.observed_criterion, not flagged as systematically absent, not flagged as unreliable |
< |
satisfies _refine.ls_d_res_high, satisfies _refine.ls_d_res_low, unobserved by _reflns.observed_criterion, not flagged as systematically absent, not flagged as unreliable |
- |
systematically absent reflection |
x |
unreliable measurement -- not used |
h |
does not satisfy _refine.ls_d_res_high |
l |
does not satisfy _refine.ls_d_res_low |
f |
satisfies _refine.ls_d_res_high, satisfies _refine.ls_d_res_low, observed by _reflns.observed_criterion, not flagged as systematically absent, not flagged as unreliable, excluded from refinement so as to be included in the calculation of a 'free' R factor |
Category: refln
Mandatory: no
The calculated structure-factor phase in degrees.
Alias: _refln_phase_calc (cif_core.dic, 2.0.1)
Type: float
Units: degrees
Category: refln
Mandatory: no
The measured structure-factor phase in degrees.
Alias: _refln_phase_meas (cif_core.dic, 2.0.1)
Type: float
Units: degrees
Category: refln
Mandatory: no
Status of a reflection in the structure-refinement process.
Alias: _refln_refinement_status (cif_core.dic, 2.0.1)
Type: ucode
Default value: incl
Enumeration values:
| Value | Detail |
|---|---|
incl |
included in ls process |
excl |
excluded from ls process |
extn |
excluded due to extinction |
Mandatory: yes
This data item is a pointer to _reflns_scale.group_code in the REFLNS_SCALE category.
Alias: _refln_scale_group_code (cif_core.dic, 2.0.1)
Category: refln
Mandatory: no
The (sin theta)/lambda value in reciprocal angstroms for this reflection.
Alias: _refln_sint/lambda (cif_core.dic, 2.0.1)
Type: float
Units: reciprocal_angstroms
Range: [0.0, .] [0.0, 0.0]
Category: refln
Mandatory: no
The symmetry reinforcement factor corresponding to the number of times the reflection indices are generated identically from the space-group symmetry operations.
Alias: _refln_symmetry_epsilon (cif_core.dic, 2.0.1)
Type: int
Range: [48, 48] [1, 48] [1, 1]
Category: refln
Mandatory: no
The number of symmetry-equivalent reflections. The equivalent reflections have the same structure-factor magnitudes because of the space-group symmetry and the Friedel relationship.
Alias: _refln_symmetry_multiplicity (cif_core.dic, 2.0.1)
Type: int
Range: [48, 48] [1, 48] [1, 1]
Category: refln
Mandatory: no
The mean wavelength in angstroms of radiation used to measure this reflection. This is an important parameter for data collected using energy-dispersive detectors or the Laue method.
Alias: _refln_wavelength (cif_core.dic, 2.0.1)
Type: float
Units: angstroms
Range: [0.0, .] [0.0, 0.0]
Mandatory: yes
This data item is a pointer to _diffrn_radiation.wavelength_id in the DIFFRN_RADIATION category.
Alias: _refln_wavelength_id (cif_core.dic, 2.0.1)
Data items in the REFLN_SYS_ABS category record details about the reflection data that should be systematically absent, given the designated space group.
Mandatory: no
Keys: _refln_sys_abs.index_h _refln_sys_abs.index_k _refln_sys_abs.index_l
Groups: inclusive_group refln_group
Examples:
| Example | Detail |
|---|---|
loop_
_refln_sys_abs.index_h
_refln_sys_abs.index_k
_refln_sys_abs.index_l
_refln_sys_abs.I
_refln_sys_abs.sigmaI
_refln_sys_abs.I_over_sigmaI
0 3 0 28.32 22.95 1.23
0 5 0 14.11 16.38 0.86
0 7 0 114.81 20.22 5.67
0 9 0 32.99 24.51 1.35
|
Example 1 - hypothetical example. |
Category: refln_sys_abs
Mandatory: no
The measured value of the intensity in arbitrary units.
Alias: _ebi_refln_sys_abs.I (ebi_extensions, 1.0)
Type: float
Type conditions: esd
Units: arbitrary
Related items: _refln_sys_abs.sigmaI (associated_esd)
Category: refln_sys_abs
Mandatory: no
The ratio of _refln_sys_abs.I to _refln_sys_abs.sigmaI. Used to evaluate whether a reflection that should be systematically absent according to the designated space group is in fact absent.
Alias: _ebi_refln_sys_abs.I_over_sigma (ebi_extensions, 1.0)
Type: float
Category: refln_sys_abs
Mandatory: yes
Sub-category: miller_index
Miller index h of the reflection. The values of the Miller indices in the REFLN_SYS_ABS category must correspond to the cell defined by cell lengths and cell angles in the CELL category.
Alias: _ebi_refln_sys_abs.h (ebi_extensions, 1.0)
Type: int
Dependent items: _refln_sys_abs.index_k _refln_sys_abs.index_l
Category: refln_sys_abs
Mandatory: yes
Sub-category: miller_index
Miller index k of the reflection. The values of the Miller indices in the REFLN_SYS_ABS category must correspond to the cell defined by cell lengths and cell angles in the CELL category.
Alias: _ebi_refln_sys_abs.k (ebi_extensions, 1.0)
Type: int
Dependent items: _refln_sys_abs.index_h _refln_sys_abs.index_l
Category: refln_sys_abs
Mandatory: yes
Sub-category: miller_index
Miller index l of the reflection. The values of the Miller indices in the REFLN_SYS_ABS category must correspond to the cell defined by cell lengths and cell angles in the CELL category.
Alias: _ebi_refln_sys_abs.l (ebi_extensions, 1.0)
Type: int
Dependent items: _refln_sys_abs.index_h _refln_sys_abs.index_k
Category: refln_sys_abs
Mandatory: no
The standard uncertainty (estimated standard deviation) of _refln_sys_abs.I in arbitrary units.
Alias: _ebi_refln_sys_abs.sigmaI (ebi_extensions, 1.0)
Type: float
Units: arbitrary
Related items: _refln_sys_abs.I (associated_value)
Data items in the REFLNS category record details about the reflection data used to determine the ATOM_SITE data items. The REFLN data items refer to individual reflections and must be included in looped lists. The REFLNS data items specify the parameters that apply to all reflections. The REFLNS data items are not looped.
Mandatory: no
Keys: _reflns.entry_id
Groups: inclusive_group refln_group
Examples:
| Example | Detail |
|---|---|
_reflns.entry_id '5HVP'
_reflns.data_reduction_method
; Xengen program scalei. Anomalous pairs were merged. Scaling
proceeded in several passes, beginning with 1-parameter
fit and ending with 3-parameter fit.
;
_reflns.data_reduction_details
; Merging and scaling based on only those reflections
with I > \s(I).
;
_reflns.d_resolution_high 2.00
_reflns.d_resolution_low 8.00
_reflns.limit_h_max 22
_reflns.limit_h_min 0
_reflns.limit_k_max 46
_reflns.limit_k_min 0
_reflns.limit_l_max 57
_reflns.limit_l_min 0
_reflns.number_obs 7228
_reflns.observed_criterion '> 1 \s(I)'
_reflns.details none
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
_reflns.limit_h_min 0
_reflns.limit_h_max 6
_reflns.limit_k_min 0
_reflns.limit_k_max 17
_reflns.limit_l_min 0
_reflns.limit_l_max 22
_reflns.number_all 1592
_reflns.number_obs 1408
_reflns.observed_criterion F_>_6.0_\s(F)
_reflns.d_resolution_high 0.8733
_reflns.d_resolution_low 11.9202
|
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. |
Category: reflns
Mandatory: no
The value of the overall isotropic displacement parameter estimated from the slope of the Wilson plot.
Type: float
Units: angstroms_squared
Mandatory: yes
This data item is a pointer to _entry.id in the ENTRY category.
Category: reflns
Mandatory: no
A description of special aspects of the data-reduction procedures.
Type: text
Example:
Merging and scaling based on only those
reflections with I > sig(I).
Category: reflns
Mandatory: no
The method used for data reduction. Note that this is not the computer program used, which is described in the SOFTWARE category, but the method itself. This data item should be used to describe significant methodological options used within the data-reduction programs.
Type: text
Example:
Profile fitting by method of Kabsch (1987).
Scaling used spherical harmonic coefficients.
Category: reflns
Mandatory: no
The smallest value for the interplanar spacings for the reflection data. This is called the highest resolution.
Alias: _reflns_d_resolution_high (cif_core.dic, 2.0.1)
Type: float
Units: angstroms
Range: [0.0, .] [0.0, 0.0]
Category: reflns
Mandatory: no
The largest value for the interplanar spacings for the reflection data. This is called the lowest resolution.
Alias: _reflns_d_resolution_low (cif_core.dic, 2.0.1)
Type: float
Units: angstroms
Range: [0.0, .] [0.0, 0.0]
Category: reflns
Mandatory: no
A description of reflection data not covered by other data names. This should include details of the Friedel pairs.
Alias: _reflns_special_details (cif_core.dic, 2.0.1)
Type: text
Category: reflns
Mandatory: no
Maximum value of the Miller index h for the reflection data. This need not have the same value as _diffrn_reflns.limit_h_max.
Alias: _reflns_limit_h_max (cif_core.dic, 2.0.1)
Type: int
Category: reflns
Mandatory: no
Minimum value of the Miller index h for the reflection data. This need not have the same value as _diffrn_reflns.limit_h_min.
Alias: _reflns_limit_h_min (cif_core.dic, 2.0.1)
Type: int
Category: reflns
Mandatory: no
Maximum value of the Miller index k for the reflection data. This need not have the same value as _diffrn_reflns.limit_k_max.
Alias: _reflns_limit_k_max (cif_core.dic, 2.0.1)
Type: int
Category: reflns
Mandatory: no
Minimum value of the Miller index k for the reflection data. This need not have the same value as _diffrn_reflns.limit_k_min.
Alias: _reflns_limit_k_min (cif_core.dic, 2.0.1)
Type: int
Category: reflns
Mandatory: no
Maximum value of the Miller index l for the reflection data. This need not have the same value as _diffrn_reflns.limit_l_max.
Alias: _reflns_limit_l_max (cif_core.dic, 2.0.1)
Type: int
Category: reflns
Mandatory: no
Minimum value of the Miller index l for the reflection data. This need not have the same value as _diffrn_reflns.limit_l_min.
Alias: _reflns_limit_l_min (cif_core.dic, 2.0.1)
Type: int
Category: reflns
Mandatory: no
The total number of reflections in the REFLN list (not the DIFFRN_REFLN list). This number may contain Friedel-equivalent reflections according to the nature of the structure and the procedures used. The item _reflns.details describes the reflection data.
Alias: _reflns_number_total (cif_core.dic, 2.0.1)
Type: int
Range: [0, .] [0, 0]
Category: reflns
Mandatory: no
The number of reflections in the REFLN list (not the DIFFRN_REFLN list) classified as observed (see _reflns.observed_criterion). This number may contain Friedel-equivalent reflections according to the nature of the structure and the procedures used.
Alias: _reflns_number_observed (cif_core.dic, 2.0.1)
Type: int
Range: [0, .] [0, 0]
Category: reflns
Mandatory: no
The criterion used to classify a reflection as 'observed'. This criterion is usually expressed in terms of a sigma(I) or sigma(F) threshold.
Alias: _reflns_observed_criterion (cif_core.dic, 2.0.1)
Type: text
Related items: _reflns.observed_criterion_sigma_F (alternate) _reflns.observed_criterion_sigma_I (alternate) _reflns.observed_criterion_I_min (alternate) _reflns.observed_criterion_I_max (alternate) _reflns.observed_criterion_F_min (alternate) _reflns.observed_criterion_F_max (alternate)
Example:
>2sigma(I)
Category: reflns
Mandatory: no
The criterion used to classify a reflection as 'observed' expressed as an upper limit for the value of F.
Type: float
Related items: _reflns.observed_criterion (alternate) _reflns.observed_criterion_I_max (convention)
Category: reflns
Mandatory: no
The criterion used to classify a reflection as 'observed' expressed as a lower limit for the value of F.
Type: float
Related items: _reflns.observed_criterion (alternate) _reflns.observed_criterion_I_min (convention)
Category: reflns
Mandatory: no
The criterion used to classify a reflection as 'observed' expressed as an upper limit for the value of I.
Type: float
Related items: _reflns.observed_criterion (alternate) _reflns.observed_criterion_F_max (convention)
Category: reflns
Mandatory: no
The criterion used to classify a reflection as 'observed' expressed as a lower limit for the value of I.
Type: float
Related items: _reflns.observed_criterion (alternate) _reflns.observed_criterion_F_min (convention)
Category: reflns
Mandatory: no
The criterion used to classify a reflection as 'observed' expressed as a multiple of the value of sigma(F).
Type: float
Related items: _reflns.observed_criterion (alternate) _reflns.observed_criterion_sigma_I (convention)
Category: reflns
Mandatory: no
The criterion used to classify a reflection as 'observed' expressed as a multiple of the value of sigma(I).
Type: float
Related items: _reflns.observed_criterion (alternate) _reflns.observed_criterion_sigma_F (convention)
Category: reflns
Mandatory: no
The percentage of geometrically possible reflections represented by reflections that satisfy the resolution limits established by _reflns.d_resolution_high and _reflns.d_resolution_low and the observation limit established by _reflns.observed_criterion.
Type: float
Range: [0.0, .] [0.0, 0.0]
Category: reflns
Mandatory: no
A description of the method by which a subset of reflections was selected for exclusion from refinement so as to be used in the calculation of a 'free' R factor.
Type: text
Example:
The data set was sorted with l varying most
rapidly and h varying least rapidly. Every
10th reflection in this sorted list was
excluded from refinement and included in the
calculation of a 'free' R factor.
Category: reflns
Mandatory: no
Residual factor Rmerge for all reflections that satisfy the resolution limits established by _reflns.d_resolution_high and _reflns.d_resolution_low. sumi(sumj|Fj - <F>|) Rmerge(F) = -------------------------- sumi(sumj<F>) Fj = the amplitude of the jth observation of reflection i <F> = the mean of the amplitudes of all observations of reflection i sumi is taken over all reflections sumj is taken over all observations of each reflection
Type: float
Range: [0.0, .] [0.0, 0.0]
Category: reflns
Mandatory: no
Residual factor Rmerge for reflections that satisfy the resolution limits established by _reflns.d_resolution_high and _reflns.d_resolution_low and the observation limit established by _reflns.observed_criterion. sumi(sumj|Fj - <F>|) Rmerge(F) = -------------------------- sumi(sumj<F>) Fj = the amplitude of the jth observation of reflection i <F> = the mean of the amplitudes of all observations of reflection i sumi is taken over all reflections sumj is taken over all observations of each reflection
Type: float
Range: [0.0, .] [0.0, 0.0]
Data items in the REFLNS_SCALE category record details about the structure-factor scales. They are referenced from within the REFLN list through _refln.scale_group_code.
Mandatory: no
Keys: _reflns_scale.group_code
Groups: inclusive_group refln_group
Examples:
| Example | Detail |
|---|---|
_reflns_scale.group_code SG1
_reflns_scale.meas_F 4.0
|
Example 1 - based on laboratory records for the collagen-like peptide [(POG)4 EKG (POG)5]3. |
| Name | Category | Mandatory |
|---|---|---|
| _reflns_scale.group_code | reflns_scale | yes |
| _refln.scale_group_code | refln | yes |
The code identifying a scale _reflns_scale.meas_F, _reflns_scale.meas_F_squared or _reflns_scale.meas_intensity. These are linked to the REFLN list by the _refln.scale_group_code. These codes need not correspond to those in the DIFFRN_SCALE list.
Alias: _reflns_scale_group_code (cif_core.dic, 2.0.1)
Type: line
Child / Parent relations:
| Child | Parent |
|---|---|
| _refln.scale_group_code | _reflns_scale.group_code |
Examples:
| Example | Detail |
|---|---|
1 |
|
2 |
|
c1 |
|
c2 |
Category: reflns_scale
Mandatory: no
A scale associated with _reflns_scale.group_code.
Alias: _reflns_scale_meas_F (cif_core.dic, 2.0.1)
Type: float
Range: [0.0, .] [0.0, 0.0]
Category: reflns_scale
Mandatory: no
A scale associated with _reflns_scale.group_code.
Alias: _reflns_scale_meas_F_squared (cif_core.dic, 2.0.1)
Type: float
Range: [0.0, .] [0.0, 0.0]
Category: reflns_scale
Mandatory: no
A scale associated with _reflns_scale.group_code.
Alias: _reflns_scale_meas_intensity (cif_core.dic, 2.0.1)
Type: float
Range: [0.0, .] [0.0, 0.0]
Data items in the REFLNS_SHELL category record details about the reflection data used to determine the ATOM_SITE data items broken down into shells of resolution.
Mandatory: no
Keys: _reflns_shell.d_res_high _reflns_shell.d_res_low
Groups: inclusive_group refln_group
Examples:
| Example | Detail |
|---|---|
loop_
_reflns_shell.d_res_high
_reflns_shell.d_res_low
_reflns_shell.meanI_over_sigI_obs
_reflns_shell.number_measured_obs
_reflns_shell.number_unique_obs
_reflns_shell.percent_possible_obs
_reflns_shell.Rmerge_F_obs
31.38 3.82 69.8 9024 2540 96.8 1.98
3.82 3.03 26.1 7413 2364 95.1 3.85
3.03 2.65 10.5 5640 2123 86.2 6.37
2.65 2.41 6.4 4322 1882 76.8 8.01
2.41 2.23 4.3 3247 1714 70.4 9.86
2.23 2.10 3.1 1140 812 33.3 13.99
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
Category: reflns_shell
Mandatory: yes
The smallest value in angstroms for the interplanar spacings for the reflections in this shell. This is called the highest resolution.
Alias: _reflns_shell_d_res_high (cif_core.dic, 2.0.1)
Type: float
Units: angstroms
Range: [0.0, .] [0.0, 0.0]
Category: reflns_shell
Mandatory: yes
The highest value in angstroms for the interplanar spacings for the reflections in this shell. This is called the lowest resolution.
Alias: _reflns_shell_d_res_low (cif_core.dic, 2.0.1)
Type: float
Units: angstroms
Range: [0.0, .] [0.0, 0.0]
Category: reflns_shell
Mandatory: no
The ratio of the mean of the intensities of all reflections in this shell to the mean of the standard uncertainties of the intensities of all reflections in this shell.
Alias: _reflns_shell_meanI_over_sigI_all (cif_core.dic, 2.0.1)
Type: float
Category: reflns_shell
Mandatory: no
The ratio of the mean of the intensities of the reflections classified as 'observed' (see _reflns.observed_criterion) in this shell to the mean of the standard uncertainties of the intensities of the 'observed' reflections in this shell.
Alias: _reflns_shell_meanI_over_sigI_obs (cif_core.dic, 2.0.1)
Type: float
Category: reflns_shell
Mandatory: no
The total number of reflections measured for this shell.
Alias: _reflns_shell_number_measured_all (cif_core.dic, 2.0.1)
Type: int
Category: reflns_shell
Mandatory: no
The number of reflections classified as 'observed' (see _reflns.observed_criterion) for this shell.
Alias: _reflns_shell_number_measured_obs (cif_core.dic, 2.0.1)
Type: int
Category: reflns_shell
Mandatory: no
The number of unique reflections it is possible to measure in this shell.
Alias: _reflns_shell_number_possible (cif_core.dic, 2.0.1)
Type: int
Range: [0, .] [0, 0]
Category: reflns_shell
Mandatory: no
The total number of measured reflections which are symmetry- unique after merging for this shell.
Alias: _reflns_shell_number_unique_all (cif_core.dic, 2.0.1)
Type: int
Category: reflns_shell
Mandatory: no
The total number of measured reflections classified as 'observed' (see _reflns.observed_criterion) which are symmetry-unique after merging for this shell.
Alias: _reflns_shell_number_unique_obs (cif_core.dic, 2.0.1)
Type: int
Category: reflns_shell
Mandatory: no
The percentage of geometrically possible reflections represented by all reflections measured for this shell.
Alias: _reflns_shell_percent_possible_all (cif_core.dic, 2.0.1)
Type: float
Range: [0.0, .] [0.0, 0.0]
Category: reflns_shell
Mandatory: no
The percentage of geometrically possible reflections represented by reflections classified as 'observed' (see _reflns.observed_criterion) for this shell.
Alias: _reflns_shell_percent_possible_obs (cif_core.dic, 2.0.1)
Type: float
Range: [0.0, .] [0.0, 0.0]
Category: reflns_shell
Mandatory: no
Residual factor Rmerge for all reflections that satisfy the resolution limits established by _reflns_shell.d_res_high and _reflns_shell.d_res_low. sumi(sumj|Fj - <F>|) Rmerge(F) = -------------------------- sumi(sumj<F>) Fj = the amplitude of the jth observation of reflection i <F> = the mean of the amplitudes of all observations of reflection i sumi is taken over all reflections sumj is taken over all observations of each reflection
Alias: _reflns_shell_Rmerge_F_all (cif_core.dic, 2.0.1)
Type: float
Range: [0.0, .] [0.0, 0.0]
Category: reflns_shell
Mandatory: no
Residual factor Rmerge for reflections that satisfy the resolution limits established by _reflns_shell.d_res_high and _reflns_shell.d_res_low and the observation criterion established by _reflns.observed_criterion. sumi(sumj|Fj - <F>|) Rmerge(F) = -------------------------- sumi(sumj<F>) Fj = the amplitude of the jth observation of reflection i <F> = the mean of the amplitudes of all observations of reflection i sumi is taken over all reflections sumj is taken over all observations of each reflection
Alias: _reflns_shell_Rmerge_F_obs (cif_core.dic, 2.0.1)
Type: float
Range: [0.0, .] [0.0, 0.0]
Category: reflns_shell
Mandatory: no
The value of Rmerge(I) for all reflections in a given shell. sumi(sumj|Ij - <I>|) Rmerge(I) = -------------------------- sumi(sumj<I>) Ij = the intensity of the jth observation of reflection i <I> = the mean of the intensities of all observations of reflection i sumi is taken over all reflections sumj is taken over all observations of each reflection
Alias: _reflns_shell_Rmerge_I_all (cif_core.dic, 2.0.1)
Type: float
Range: [0.0, .] [0.0, 0.0]
Category: reflns_shell
Mandatory: no
The value of Rmerge(I) for reflections classified as 'observed' (see _reflns.observed_criterion) in a given shell. sumi(sumj|Ij - <I>|) Rmerge(I) = -------------------------- sumi(sumj<I>) Ij = the intensity of the jth observation of reflection i <I> = the mean of the intensities of all observations of reflection i sumi is taken over all reflections sumj is taken over all observations of each reflection
Alias: _reflns_shell_Rmerge_I_obs (cif_core.dic, 2.0.1)
Type: float
Range: [0.0, .] [0.0, 0.0]
Data items in the SOFTWARE category record details about the software used in the structure analysis, which implies any software used in the generation of any data items associated with the structure determination and structure representation. These data items allow computer programs to be referenced in more detail than data items in the COMPUTING category do.
Mandatory: no
Keys: _software.name _software.version
Groups: inclusive_group computing_group
Examples:
| Example | Detail |
|---|---|
loop_
_software.name
_software.version
_software.date
_software.type
_software.contact_author
_software.contact_author_email
_software.location
_software.classification
_software.citation_id
_software.language
_software.compiler_name
_software.compiler_version
_software.hardware
_software.os
_software.os_version
_software.dependencies
_software.mods
_software.description
Prolsq unknown . program 'Wayne A. Hendrickson' ?
'ftp://rosebud.sdsc.edu/pub/sdsc/xtal/CCP4/ccp4/'
refinement ref5 Fortran
'Convex Fortran' v8.0 'Convex C220' ConvexOS v10.1
'Requires that Protin be run first' optimized
'restrained least-squares refinement'
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
Mandatory: no
This data item is a pointer to _citation.id in the CITATION category.
Category: software
Mandatory: no
The classification of the program according to its major function.
Type: uline
Examples:
| Example | Detail |
|---|---|
data collection |
|
data reduction |
|
phasing |
|
model building |
|
refinement |
|
validation |
|
other |
Category: software
Mandatory: no
The compiler used to compile the software.
Type: line
Examples:
| Example | Detail |
|---|---|
Convex Fortran |
|
gcc |
|
DEC C |
Category: software
Mandatory: no
The version of the compiler used to compile the software.
Type: line
Examples:
| Example | Detail |
|---|---|
3.1 |
|
2.1 alpha |
Category: software
Mandatory: no
The recognized contact author of the software. This could be the original author, someone who has modified the code or someone who maintains the code. It should be the person most commonly associated with the code.
Type: line
Examples:
| Example | Detail |
|---|---|
T. Alwyn Jones |
|
Axel Brunger |
Category: software
Mandatory: no
The e-mail address of the person specified in _software.contact_author.
Type: line
Example:
bourne@sdsc.edu
Category: software
Mandatory: no
The date the software was released.
Type: line
Examples:
| Example | Detail |
|---|---|
1991-10-01 |
|
1990-04-30 |
Category: software
Mandatory: no
Description of the software.
Type: line
Example:
Uses method of restrained least squares
Category: software
Mandatory: no
Any prerequisite software required to run _software.name.
Type: line
Example:
PDBlib class library
Category: software
Mandatory: no
The hardware upon which the software was run.
Type: line
Examples:
| Example | Detail |
|---|---|
Sun Sparc 10 model 41 |
|
Dec Alpha 3000 model 500S |
|
Silicon Graphics Elan |
|
Compaq PC 486/66 |
Category: software
Mandatory: no
The major computing language in which the software is coded.
Type: uline
Enumeration values:
| Value | Detail |
|---|---|
Ada |
|
assembler |
|
Awk |
|
Basic |
|
C++ |
|
C/C++ |
|
C |
|
csh |
|
Fortran |
|
Fortran_77 |
|
Fortran 77 |
|
Fortran 90 |
|
Java |
|
ksh |
|
Pascal |
|
Perl |
|
Python |
|
sh |
|
Tcl |
|
Other |
Category: software
Mandatory: no
The URL for an Internet address at which details of the software can be found.
Type: line
Examples:
| Example | Detail |
|---|---|
http://rosebud.sdsc.edu/projects/pb/IUCr/software.html |
|
ftp://ftp.sdsc.edu/pub/sdsc/biology/ |
Category: software
Mandatory: no
Any noteworthy modifications to the base software, if applicable.
Type: line
Example:
Added support for space group F432
Category: software
Mandatory: yes
The name of the software.
Type: text
Examples:
| Example | Detail |
|---|---|
Merlot |
|
O |
|
Xengen |
|
X-plor |
Category: software
Mandatory: no
The name of the operating system under which the software runs.
Type: text
Examples:
| Example | Detail |
|---|---|
Ultrix |
|
OpenVMS |
|
DOS |
|
Windows 95 |
|
Windows NT |
|
Irix |
|
HPUX |
|
DEC Unix |
Category: software
Mandatory: no
The version of the operating system under which the software runs.
Type: text
Examples:
| Example | Detail |
|---|---|
3.1 |
|
4.2.1 |
Category: software
Mandatory: no
The classification of the software according to the most common types.
Type: uline
Enumeration values:
| Value | Detail |
|---|---|
program |
individual program with limited functionality |
library |
used by a program at load time |
package |
collections of programs with multiple functionality |
filter |
filters input and output streams |
jiffy |
short, simple program |
other |
all other kinds of software |
Category: software
Mandatory: yes
The version of the software.
Type: line
Examples:
| Example | Detail |
|---|---|
v1.0 |
|
beta |
|
3.1-2 |
|
unknown |
Data items in the STRUCT category record details about the description of the crystallographic structure.
Mandatory: no
Keys: _struct.entry_id
Groups: inclusive_group struct_group
Examples:
| Example | Detail |
|---|---|
_struct.entry_id '5HVP'
_struct.title
; HIV-1 protease complex with acetyl-pepstatin
;
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
Mandatory: yes
This data item is a pointer to _entry.id in the ENTRY category.
Category: struct
Mandatory: no
A title for the data block. The author should attempt to convey the essence of the structure archived in the CIF in the title, and to distinguish this structural result from others.
Type: text
Examples:
| Example | Detail |
|---|---|
5'-D(*(I)CP*CP*GP*G)-3 |
|
T4 lysozyme mutant - S32A |
|
hen egg white lysozyme at -30 degrees C |
|
quail egg white lysozyme at 2 atmospheres |
Data items in the STRUCT_ASYM category record details about the structural elements in the asymmetric unit.
Mandatory: no
Keys: _struct_asym.id
Groups: inclusive_group struct_group
Examples:
| Example | Detail |
|---|---|
loop_
_struct_asym.id
_struct_asym.entity_id
_struct_asym.details
A 1 'one monomer of the dimeric enzyme'
B 1 'one monomer of the dimeric enzyme'
C 2 'one partially occupied position for the inhibitor'
D 2 'one partially occupied position for the inhibitor'
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
Category: struct_asym
Mandatory: no
A description of special aspects of this portion of the contents of the asymmetric unit.
Type: text
Example:
The drug binds to this enzyme in two roughly
twofold symmetric modes. Hence this
biological unit (3) is roughly twofold
symmetric to biological unit (2). Disorder in
the protein chain indicated with alternative
ID 2 should be used with this biological unit.
Mandatory: yes
This data item is a pointer to _entity.id in the ENTITY category.
| Name | Category | Mandatory |
|---|---|---|
| _struct_asym.id | struct_asym | yes |
| _atom_site.label_asym_id | atom_site | no |
| _geom_angle.atom_site_label_asym_id_1 | geom_angle | no |
| _geom_angle.atom_site_label_asym_id_2 | geom_angle | no |
| _geom_angle.atom_site_label_asym_id_3 | geom_angle | no |
| _geom_bond.atom_site_label_asym_id_1 | geom_bond | no |
| _geom_bond.atom_site_label_asym_id_2 | geom_bond | no |
| _geom_contact.atom_site_label_asym_id_1 | geom_contact | no |
| _geom_contact.atom_site_label_asym_id_2 | geom_contact | no |
| _geom_hbond.atom_site_label_asym_id_A | geom_hbond | no |
| _geom_hbond.atom_site_label_asym_id_D | geom_hbond | no |
| _geom_hbond.atom_site_label_asym_id_H | geom_hbond | no |
| _geom_torsion.atom_site_label_asym_id_1 | geom_torsion | no |
| _geom_torsion.atom_site_label_asym_id_2 | geom_torsion | no |
| _geom_torsion.atom_site_label_asym_id_3 | geom_torsion | no |
| _geom_torsion.atom_site_label_asym_id_4 | geom_torsion | no |
| _struct_biol_gen.asym_id | struct_biol_gen | yes |
| _struct_conf.beg_label_asym_id | struct_conf | yes |
| _struct_conf.end_label_asym_id | struct_conf | yes |
| _struct_conn.ptnr1_label_asym_id | struct_conn | yes |
| _struct_conn.ptnr2_label_asym_id | struct_conn | yes |
| _struct_mon_nucl.label_asym_id | struct_mon_nucl | yes |
| _struct_mon_prot.label_asym_id | struct_mon_prot | yes |
| _struct_mon_prot_cis.label_asym_id | struct_mon_prot_cis | yes |
| _struct_ncs_dom_lim.beg_label_asym_id | struct_ncs_dom_lim | yes |
| _struct_ncs_dom_lim.end_label_asym_id | struct_ncs_dom_lim | yes |
| _struct_sheet_range.beg_label_asym_id | struct_sheet_range | yes |
| _struct_sheet_range.end_label_asym_id | struct_sheet_range | yes |
| _struct_site_gen.label_asym_id | struct_site_gen | yes |
The value of _struct_asym.id must uniquely identify a record in the STRUCT_ASYM list. Note that this item need not be a number; it can be any unique identifier.
Type: code
Child / Parent relations:
Examples:
| Example | Detail |
|---|---|
1 |
|
A |
|
2B3 |
Data items in the STRUCT_BIOL category record details about the structural elements that form each structure of biological significance. A given crystal structure may contain many different biological structures. A given structural component in the asymmetric unit may be part of more than one biological unit. A given biological structure may involve crystallographic symmetry. For instance, in a structure of a lysozyme-FAB structure, the light- and heavy-chain components of the FAB could be one biological unit, while the two chains of the FAB and the lysozyme could constitute a second biological unit.
Mandatory: no
Keys: _struct_biol.id
Groups: inclusive_group struct_group
Examples:
| Example | Detail |
|---|---|
loop_
_struct_biol.id
_struct_biol.details
1
; significant deviations from twofold symmetry exist in this
dimeric enzyme
;
2
; The drug binds to this enzyme in two roughly twofold
symmetric modes. Hence this biological unit (2) is roughly
twofold symmetric to biological unit (3). Disorder in the
protein chain indicated with alternative ID 1 should be
used with this biological unit.
;
3
; The drug binds to this enzyme in two roughly twofold
symmetric modes. Hence this biological unit (3) is roughly
twofold symmetric to biological unit (2). Disorder in the
protein chain indicated with alternative ID 2 should be
used with this biological unit.
;
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
Category: struct_biol
Mandatory: no
A description of special aspects of the biological unit.
Type: text
Example:
The drug binds to this enzyme in two roughly
twofold symmetric modes. Hence this
biological unit (3) is roughly twofold
symmetric to biological unit (2). Disorder in
the protein chain indicated with alternative
ID 2 should be used with this biological unit.
| Name | Category | Mandatory |
|---|---|---|
| _struct_biol.id | struct_biol | yes |
| _struct_biol_gen.biol_id | struct_biol_gen | yes |
| _struct_biol_keywords.biol_id | struct_biol_keywords | yes |
| _struct_biol_view.biol_id | struct_biol_view | yes |
| _struct_ref.biol_id | struct_ref | no |
The value of _struct_biol.id must uniquely identify a record in the STRUCT_BIOL list. Note that this item need not be a number; it can be any unique identifier.
Type: line
Child / Parent relations:
| Child | Parent |
|---|---|
| _struct_biol_gen.biol_id | _struct_biol.id |
| _struct_biol_keywords.biol_id | _struct_biol.id |
| _struct_biol_view.biol_id | _struct_biol.id |
| _struct_ref.biol_id | _struct_biol.id |
Data items in the STRUCT_BIOL_GEN category record details about the generation of each biological unit. The STRUCT_BIOL_GEN data items provide the specifications of the components that constitute that biological unit, which may include symmetry elements.
Mandatory: no
Keys: _struct_biol_gen.biol_id _struct_biol_gen.asym_id _struct_biol_gen.symmetry
Groups: inclusive_group struct_group
Examples:
| Example | Detail |
|---|---|
loop_
_struct_biol_gen.biol_id
_struct_biol_gen.asym_id
_struct_biol_gen.symmetry
1 A 1_555
1 B 1_555
2 A 1_555
2 B 1_555
2 C 1_555
3 A 1_555
3 B 1_555
3 D 1_555
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
Mandatory: yes
This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category.
Mandatory: yes
This data item is a pointer to _struct_biol.id in the STRUCT_BIOL category.
Category: struct_biol_gen
Mandatory: no
A description of special aspects of the symmetry generation of this portion of the biological structure.
Type: text
Example:
The zinc atom lies on a special position;
application of symmetry elements to generate
the insulin hexamer will generate excess zinc
atoms, which must be removed by hand.
Category: struct_biol_gen
Mandatory: yes
Describes the symmetry operation that should be applied to the atom set specified by _struct_biol_gen.asym_id to generate a portion of the biological structure.
Type: symop
Examples:
| Example | Detail |
|---|---|
. |
no symmetry or translation to site |
4 |
4th symmetry operation applied |
7_645 |
7th symm. posn.; +a on x; -b on y |
Data items in the STRUCT_BIOL_KEYWORDS category record keywords that describe each biological unit.
Mandatory: no
Keys: _struct_biol_keywords.biol_id _struct_biol_keywords.text
Groups: inclusive_group struct_group
Examples:
| Example | Detail |
|---|---|
loop_
_struct_biol_keywords.biol_id
_struct_biol_keywords.text
1 'aspartyl-protease'
1 'aspartic-protease'
1 'acid-protease'
1 'aspartyl-proteinase'
1 'aspartic-proteinase'
1 'acid-proteinase'
1 'enzyme'
1 'protease'
1 'proteinase'
1 'dimer'
2 'drug-enzyme complex'
2 'inhibitor-enzyme complex'
2 'drug-protease complex'
2 'inhibitor-protease complex'
3 'drug-enzyme complex'
3 'inhibitor-enzyme complex'
3 'drug-protease complex'
3 'inhibitor-protease complex'
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
Mandatory: yes
This data item is a pointer to _struct_biol.id in the STRUCT_BIOL category.
Category: struct_biol_keywords
Mandatory: yes
Keywords describing this biological entity.
Type: text
Examples:
| Example | Detail |
|---|---|
antibody |
|
antigen |
|
enzyme |
|
cytokine |
|
tRNA |
Data items in the STRUCT_BIOL_VIEW category record details about how to draw and annotate an informative view of the biological structure.
Mandatory: no
Keys: _struct_biol_view.biol_id _struct_biol_view.id
Groups: inclusive_group struct_group
Examples:
| Example | Detail |
|---|---|
_struct_biol_view.biol_id c1
_struct_biol_view.id 1
_struct_biol_view.rot_matrix[1][1] 0.132
_struct_biol_view.rot_matrix[1][2] 0.922
_struct_biol_view.rot_matrix[1][3] -0.363
_struct_biol_view.rot_matrix[2][1] 0.131
_struct_biol_view.rot_matrix[2][2] -0.380
_struct_biol_view.rot_matrix[2][3] -0.916
_struct_biol_view.rot_matrix[3][1] -0.982
_struct_biol_view.rot_matrix[3][2] 0.073
_struct_biol_view.rot_matrix[3][3] -0.172
_struct_biol_view.details
; This view highlights the ATAT-Netropsin interaction in the
DNA-drug complex.
;
|
Example 1 - based on NDB structure GDL001 by Coll, Aymami, Van Der Marel, Van Boom, Rich & Wang [Biochemistry, (1989), 28, 310-320]. |
Mandatory: yes
This data item is a pointer to _struct_biol.id in the STRUCT_BIOL category.
Category: struct_biol_view
Mandatory: no
A description of special aspects of this view of the biological structure. This data item can be used as a figure legend.
Type: text
Example:
The enzyme has been oriented with the
molecular twofold axis aligned with the
horizontal axis of the figure.
Category: struct_biol_view
Mandatory: yes
The value of _struct_biol_view.id must uniquely identify a record in the STRUCT_BIOL_VIEW list. Note that this item need not be a number; it can be any unique identifier.
Type: line
Examples:
| Example | Detail |
|---|---|
Figure 1 |
|
unliganded enzyme |
|
view down enzyme active site |
Category: struct_biol_view
Mandatory: no
Sub-category: matrix
The [1][1] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_BIOL_GEN category to give a view useful for describing the structure. The conventions used in the rotation are described in _struct_biol_view.details. |x'| |11 12 13| |x| |y'|reoriented Cartesian = |21 22 23| |y|Cartesian |z'| |31 32 33| |z|
Type: float
Category: struct_biol_view
Mandatory: no
Sub-category: matrix
The [1][2] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_BIOL_GEN category to give a view useful for describing the structure. The conventions used in the rotation are described in _struct_biol_view.details. |x'| |11 12 13| |x| |y'|reoriented Cartesian = |21 22 23| |y|Cartesian |z'| |31 32 33| |z|
Type: float
Category: struct_biol_view
Mandatory: no
Sub-category: matrix
The [1][3] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_BIOL_GEN category to give a view useful for describing the structure. The conventions used in the rotation are described in _struct_biol_view.details. |x'| |11 12 13| |x| |y'|reoriented Cartesian = |21 22 23| |y|Cartesian |z'| |31 32 33| |z|
Type: float
Category: struct_biol_view
Mandatory: no
Sub-category: matrix
The [2][1] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_BIOL_GEN category to give a view useful for describing the structure. The conventions used in the rotation are described in _struct_biol_view.details. |x'| |11 12 13| |x| |y'|reoriented Cartesian = |21 22 23| |y|Cartesian |z'| |31 32 33| |z|
Type: float
Category: struct_biol_view
Mandatory: no
Sub-category: matrix
The [2][2] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_BIOL_GEN category to give a view useful for describing the structure. The conventions used in the rotation are described in _struct_biol_view.details. |x'| |11 12 13| |x| |y'|reoriented Cartesian = |21 22 23| |y|Cartesian |z'| |31 32 33| |z|
Type: float
Category: struct_biol_view
Mandatory: no
Sub-category: matrix
The [2][3] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_BIOL_GEN category to give a view useful for describing the structure. The conventions used in the rotation are described in _struct_biol_view.details. |x'| |11 12 13| |x| |y'|reoriented Cartesian = |21 22 23| |y|Cartesian |z'| |31 32 33| |z|
Type: float
Category: struct_biol_view
Mandatory: no
Sub-category: matrix
The [3][1] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_BIOL_GEN category to give a view useful for describing the structure. The conventions used in the rotation are described in _struct_biol_view.details. |x'| |11 12 13| |x| |y'|reoriented Cartesian = |21 22 23| |y|Cartesian |z'| |31 32 33| |z|
Type: float
Category: struct_biol_view
Mandatory: no
Sub-category: matrix
The [3][2] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_BIOL_GEN category to give a view useful for describing the structure. The conventions used in the rotation are described in _struct_biol_view.details. |x'| |11 12 13| |x| |y'|reoriented Cartesian = |21 22 23| |y|Cartesian |z'| |31 32 33| |z|
Type: float
Category: struct_biol_view
Mandatory: no
Sub-category: matrix
The [3][3] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_BIOL_GEN category to give a view useful for describing the structure. The conventions used in the rotation are described in _struct_biol_view.details. |x'| |11 12 13| |x| |y'|reoriented Cartesian = |21 22 23| |y|Cartesian |z'| |31 32 33| |z|
Type: float
Data items in the STRUCT_CONF category record details about the backbone conformation of a segment of polymer. Data items in the STRUCT_CONF_TYPE category define the criteria used to identify the backbone conformations.
Mandatory: no
Keys: _struct_conf.id
Groups: inclusive_group struct_group
Examples:
| Example | Detail |
|---|---|
loop_
_struct_conf.id
_struct_conf.conf_type_id
_struct_conf.beg_label_comp_id
_struct_conf.beg_label_asym_id
_struct_conf.beg_label_seq_id
_struct_conf.end_label_comp_id
_struct_conf.end_label_asym_id
_struct_conf.end_label_seq_id
_struct_conf.details
HELX1 HELX_RH_AL_P ARG A 87 GLN A 92 .
HELX2 HELX_RH_AL_P ARG B 287 GLN B 292 .
STRN1 STRN_P PRO A 1 LEU A 5 .
STRN2 STRN_P CYS B 295 PHE B 299 .
STRN3 STRN_P CYS A 95 PHE A 299 .
STRN4 STRN_P PRO B 201 LEU B 205 .
# - - - - data truncated for brevity - - - -
TURN1 TURN_TY1P_P ILE A 15 GLN A 18 .
TURN2 TURN_TY2_P GLY A 49 GLY A 52 .
TURN3 TURN_TY1P_P ILE A 55 HIS A 69 .
TURN4 TURN_TY1_P THR A 91 GLY A 94 .
# - - - - data truncated for brevity - - - -
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
Mandatory: yes
A component of the identifier for the residue at which the conformation segment begins. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category.
Mandatory: yes
A component of the identifier for the residue at which the conformation segment begins. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category.
Mandatory: yes
A component of the identifier for the residue at which the conformation segment begins. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category.
Mandatory: no
A component of the identifier for the residue at which the conformation segment begins. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category.
Mandatory: no
A component of the identifier for the residue at which the conformation segment begins. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category.
Mandatory: no
A component of the identifier for the residue at which the conformation segment begins. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category.
Mandatory: yes
This data item is a pointer to _struct_conf_type.id in the STRUCT_CONF_TYPE category.
Category: struct_conf
Mandatory: no
A description of special aspects of the conformation assignment.
Type: text
Mandatory: yes
A component of the identifier for the residue at which the conformation segment ends. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category.
Mandatory: yes
A component of the identifier for the residue at which the conformation segment ends. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category.
Mandatory: yes
A component of the identifier for the residue at which the conformation segment ends. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category.
Mandatory: no
A component of the identifier for the residue at which the conformation segment ends. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category.
Mandatory: no
A component of the identifier for the residue at which the conformation segment ends. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category.
Mandatory: no
A component of the identifier for the residue at which the conformation segment ends. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category.
Category: struct_conf
Mandatory: yes
The value of _struct_conf.id must uniquely identify a record in the STRUCT_CONF list. Note that this item need not be a number; it can be any unique identifier.
Type: code
Data items in the STRUCT_CONF_TYPE category record details about the criteria used to identify backbone conformations of a segment of polymer.
Mandatory: no
Keys: _struct_conf_type.id
Groups: inclusive_group struct_group
Examples:
| Example | Detail |
|---|---|
loop_
_struct_conf_type.id
_struct_conf_type.criteria
_struct_conf_type.reference
HELX_RH_AL_P 'author judgement' .
STRN_P 'author judgement' .
TURN_TY1_P 'author judgement' .
TURN_TY1P_P 'author judgement' .
TURN_TY2_P 'author judgement' .
TURN_TY2P_P 'author judgement' .
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
Category: struct_conf_type
Mandatory: no
The criteria used to assign this conformation type.
Type: text
Examples:
| Example | Detail |
|---|---|
author judgement |
|
phi=54-74, psi=30-50 |
| Name | Category | Mandatory |
|---|---|---|
| _struct_conf_type.id | struct_conf_type | yes |
| _struct_conf.conf_type_id | struct_conf | yes |
The descriptor that categorizes the type of the conformation of the backbone of the polymer (whether protein or nucleic acid). Explicit values for the torsion angles that define each conformation are not given here, but it is expected that the author would provide such information in either the _struct_conf_type.criteria or _struct_conf_type.reference data items, or both.
Type: ucode
Child / Parent relations:
| Child | Parent |
|---|---|
| _struct_conf.conf_type_id | _struct_conf_type.id |
Enumeration values:
| Value | Detail |
|---|---|
HELX_P |
helix with handedness and type not specified (protein) |
HELX_OT_P |
helix with handedness and type that do not conform to an accepted category (protein) |
HELX_RH_P |
right-handed helix with type not specified (protein) |
HELX_RH_OT_P |
right-handed helix with type that does not conform to an accepted category (protein) |
HELX_RH_AL_P |
right-handed alpha helix (protein) |
HELX_RH_GA_P |
right-handed gamma helix (protein) |
HELX_RH_OM_P |
right-handed omega helix (protein) |
HELX_RH_PI_P |
right-handed pi helix (protein) |
HELX_RH_27_P |
right-handed 2-7 helix (protein) |
HELX_RH_3T_P |
right-handed 3-10 helix (protein) |
HELX_RH_PP_P |
right-handed polyproline helix (protein) |
HELX_LH_P |
left-handed helix with type not specified (protein) |
HELX_LH_OT_P |
left-handed helix with type that does not conform to an accepted category (protein) |
HELX_LH_AL_P |
left-handed alpha helix (protein) |
HELX_LH_GA_P |
left-handed gamma helix (protein) |
HELX_LH_OM_P |
left-handed omega helix (protein) |
HELX_LH_PI_P |
left-handed pi helix (protein) |
HELX_LH_27_P |
left-handed 2-7 helix (protein) |
HELX_LH_3T_P |
left-handed 3-10 helix (protein) |
HELX_LH_PP_P |
left-handed polyproline helix (protein) |
HELX_N |
helix with handedness and type not specified (nucleic acid) |
HELX_OT_N |
helix with handedness and type that do not conform to an accepted category (nucleic acid) |
HELX_RH_N |
right-handed helix with type not specified (nucleic acid) |
HELX_RH_OT_N |
right-handed helix with type that does not conform to an accepted category (nucleic acid) |
HELX_RH_A_N |
right-handed A helix (nucleic acid) |
HELX_RH_B_N |
right-handed B helix (nucleic acid) |
HELX_RH_Z_N |
right-handed Z helix (nucleic acid) |
HELX_LH_N |
left-handed helix with type not specified (nucleic acid) |
HELX_LH_OT_N |
left-handed helix with type that does not conform to an accepted category (nucleic acid) |
HELX_LH_A_N |
left-handed A helix (nucleic acid) |
HELX_LH_B_N |
left-handed B helix (nucleic acid) |
HELX_LH_Z_N |
left-handed Z helix (nucleic acid) |
TURN_P |
turn with type not specified (protein) |
TURN_OT_P |
turn with type that does not conform to an accepted category (protein) |
TURN_TY1_P |
type I turn (protein) |
TURN_TY1P_P |
type I prime turn (protein) |
TURN_TY2_P |
type II turn (protein) |
TURN_TY2P_P |
type II prime turn (protein) |
TURN_TY3_P |
type III turn (protein) |
TURN_TY3P_P |
type III prime turn (protein) |
STRN |
beta strand (protein) |
Category: struct_conf_type
Mandatory: no
A literature reference that defines the criteria used to assign this conformation type and subtype.
Type: text
Data items in the STRUCT_CONN category record details about the connections between portions of the structure. These can be hydrogen bonds, salt bridges, disulfide bridges and so on. The STRUCT_CONN_TYPE records define the criteria used to identify these connections.
Mandatory: no
Keys: _struct_conn.id
Groups: inclusive_group struct_group
Examples:
| Example | Detail |
|---|---|
loop_
_struct_conn.id
_struct_conn.conn_type_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_role
_struct_conn.ptnr1_symmetry
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_seq_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_role
_struct_conn.ptnr2_symmetry
_struct_conn.details
C1 saltbr ARG A 87 NZ1 positive 1_555 GLU A 92 OE1
negative 1_555 .
C2 hydrog ARG B 287 N donor 1_555 GLY B 292 O
acceptor 1_555 .
# - - - - data truncated for brevity - - - -
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
Mandatory: yes
This data item is a pointer to _struct_conn_type.id in the STRUCT_CONN_TYPE category.
Category: struct_conn
Mandatory: no
A description of special aspects of the connection.
Type: text
Example:
disulfide bridge C-S-S-C is highly distorted
Category: struct_conn
Mandatory: yes
The value of _struct_conn.id must uniquely identify a record in the STRUCT_CONN list. Note that this item need not be a number; it can be any unique identifier.
Type: code
Mandatory: no
A component of the identifier for partner 1 of the structure connection. This data item is a pointer to _atom_sites_alt.id in the ATOM_SITES_ALT category.
Mandatory: yes
A component of the identifier for partner 1 of the structure connection. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category.
Mandatory: yes
A component of the identifier for partner 1 of the structure connection. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category.
Mandatory: yes
A component of the identifier for partner 1 of the structure connection. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category.
Mandatory: yes
A component of the identifier for partner 1 of the structure connection. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category.
Mandatory: no
A component of the identifier for partner 1 of the structure connection. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category.
Mandatory: no
A component of the identifier for partner 1 of the structure connection. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category.
Mandatory: no
A component of the identifier for partner 1 of the structure connection. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category.
Mandatory: no
A component of the identifier for partner 1 of the structure connection. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category.
Category: struct_conn
Mandatory: no
The chemical or structural role of the first partner in the structure connection.
Type: uline
Examples:
| Example | Detail |
|---|---|
donor |
|
acceptor |
|
negative |
|
positive |
|
metal |
|
metal coordination |
Category: struct_conn
Mandatory: no
Describes the symmetry operation that should be applied to the atom set specified by _struct_conn.ptnr1_label* to generate the first partner in the structure connection.
Type: symop
Examples:
| Example | Detail |
|---|---|
. |
no symmetry or translation to site |
4 |
4th symmetry operation applied |
7_645 |
7th symm. posn.; +a on x; -b on y |
Mandatory: no
A component of the identifier for partner 2 of the structure connection. This data item is a pointer to _atom_sites_alt.id in the ATOM_SITES_ALT category.
Mandatory: yes
A component of the identifier for partner 2 of the structure connection. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category.
Mandatory: yes
A component of the identifier for partner 2 of the structure connection. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category.
Mandatory: yes
A component of the identifier for partner 2 of the structure connection. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category.
Mandatory: yes
A component of the identifier for partner 2 of the structure connection. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category.
Mandatory: no
A component of the identifier for partner 2 of the structure connection. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category.
Mandatory: no
A component of the identifier for partner 2 of the structure connection. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category.
Mandatory: no
A component of the identifier for partner 2 of the structure connection. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category.
Mandatory: no
A component of the identifier for partner 2 of the structure connection. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category.
Category: struct_conn
Mandatory: no
The chemical or structural role of the second partner in the structure connection.
Type: uline
Examples:
| Example | Detail |
|---|---|
donor |
|
acceptor |
|
negative |
|
positive |
|
metal |
|
metal coordination |
Category: struct_conn
Mandatory: no
Describes the symmetry operation that should be applied to the atom set specified by _struct_conn.ptnr2_label* to generate the second partner in the structure connection.
Type: symop
Examples:
| Example | Detail |
|---|---|
. |
no symmetry or translation to site |
4 |
4th symmetry operation applied |
7_645 |
7th symm. posn.; +a on x; -b on y |
Data items in the STRUCT_CONN_TYPE category record details about the criteria used to identify interactions between portions of the structure.
Mandatory: no
Keys: _struct_conn_type.id
Groups: inclusive_group struct_group
Examples:
| Example | Detail |
|---|---|
loop_
_struct_conn_type.id
_struct_conn_type.criteria
_struct_conn_type.reference
saltbr
'negative to positive distance > 2.5 \%A, < 3.2 \%A' .
hydrog
'NO distance > 2.5\%A, < 3.5\%A, NOC angle < 120 degrees' .
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
Category: struct_conn_type
Mandatory: no
The criteria used to define the interaction.
Type: text
Examples:
| Example | Detail |
|---|---|
O to N distance > 2.5 \%A, < 3.2 \%A |
|
authors judgement |
| Name | Category | Mandatory |
|---|---|---|
| _struct_conn_type.id | struct_conn_type | yes |
| _struct_conn.conn_type_id | struct_conn | yes |
The chemical or structural type of the interaction.
Type: ucode
Child / Parent relations:
| Child | Parent |
|---|---|
| _struct_conn.conn_type_id | _struct_conn_type.id |
Enumeration values:
| Value | Detail |
|---|---|
covale |
covalent bond |
disulf |
disulfide bridge |
hydrog |
hydrogen bond |
metalc |
metal coordination |
mismat |
mismatched base pairs |
saltbr |
ionic interaction |
modres |
covalent residue modification |
covale_base |
covalent modification of a nucleotide base |
covale_sugar |
covalent modification of a nucleotide sugar |
covale_phosphate |
covalent modification of a nucleotide phosphate |
Category: struct_conn_type
Mandatory: no
A reference that specifies the criteria used to define the interaction.
Type: text
Data items in the STRUCT_KEYWORDS category specify keywords that describe the chemical structure in this entry.
Mandatory: no
Keys: _struct_keywords.entry_id
Groups: inclusive_group struct_group
Examples:
| Example | Detail |
|---|---|
loop_
_struct_keywords.entry_id
_struct_keywords.text
'5HVP' 'enzyme-inhibitor complex'
'5HVP' 'aspartyl protease'
'5HVP' 'structure-based drug design'
'5HVP' 'static disorder'
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
Mandatory: yes
This data item is a pointer to _entry.id in the ENTRY category.
Category: struct_keywords
Mandatory: no
Keywords describing this structure.
Type: text
Examples:
| Example | Detail |
|---|---|
serine protease |
|
inhibited complex |
|
high-resolution refinement |
Data items in the STRUCT_MON_DETAILS category record details about specifics of calculations summarized in data items in the STRUCT_MON_PROT and STRUCT_MON_NUCL categories. These can include the coefficients used in map calculations, the radii used for including points in a calculation and so on.
Mandatory: no
Keys: _struct_mon_details.entry_id
Groups: inclusive_group struct_group
Mandatory: yes
This data item is a pointer to _entry.id in the ENTRY category.
Category: struct_mon_details
Mandatory: no
An ideal cis peptide bond would have an omega torsion angle of zero. This data item gives the value in degrees by which the observed torsion angle can differ from 0.0 and still be considered cis.
Type: float
Units: degrees
Example:
30.0
Category: struct_mon_details
Mandatory: no
This data item describes the specifics of the calculations that generated the values given in _struct_mon_prot.RSCC_all, _struct_mon_prot.RSCC_main and _struct_mon_prot.RSCC_side. The coefficients used to calculate the p(o) and p(c) maps should be given as well as the criterion for the inclusion of map grid points in the calculation.
Type: text
Examples:
| Example | Detail |
|---|---|
The map p(o) was calculated with coefficients
2F(o) - F(c) and with phase alpha(c). F(o)
are the observed structure-factor amplitudes,
F(c) are the amplitudes calculated from the
current model and alpha(c) are the phases
calculated from the current model.
The map p(c) was calculated in program O using
a Gaussian distribution function around the
atoms in the current model.
Map grid points within 1.5 A of the
designated atoms were included in the
calculation.
|
|
The map p(o) was calculated with coefficients
F(o) and with phase alpha(c). F(o) are the
observed structure-factor amplitudes, and
alpha(c) are the phases calculated from the
current model.
The map p(c) was calculated with coefficients
F(c) and with phases alpha(c). F(c) and
alpha(c) are the structure-factor amplitudes
and phases, respectively, calculated from the
current model.
Map grid points within a van der Waals radius
of the designated atoms were included in the
calculation.
|
Category: struct_mon_details
Mandatory: no
This data item describes the specifics of the calculations that generated the values given in _struct_mon_prot.RSR_all, _struct_mon_prot.RSR_main and _struct_mon_prot.RSR_side. The coefficients used to calculate the p(o) and p(c) maps should be given as well as the criterion for the inclusion of map grid points in the calculation.
Type: text
Examples:
| Example | Detail |
|---|---|
The map p(o) was calculated with coefficients
2F(o) - F(c) and with phase alpha(c). F(o)
are the observed structure-factor amplitudes,
F(c) are the amplitudes calculated from the
current model and alpha(c) are the phases
calculated from the current model.
The map p(c) was calculated in program O using
a Gaussian distribution function around the
atoms in the current model.
Map grid points within 1.5 A of the
designated atoms were included in the
calculation.
|
|
The map p(o) was calculated with coefficients
F(o) and with phase alpha(c). F(o) are the
observed structure-factor amplitudes, and
alpha(c) are the phases calculated from the
current model.
The map p(c) was calculated with coefficients
F(c) and with phases alpha(c). F(c) and
alpha(c) are the structure-factor amplitudes
and phases, respectively, calculated from the
current model.
Map grid points within a van der Waals radius
of the designated atoms were included in the
calculation.
|
Data items in the STRUCT_MON_NUCL category record details about structural properties of a nucleic acid when analyzed at the monomer level. Analogous data items for proteins are given in the STRUCT_MON_PROT category. For items where the value of the property depends on the method employed to calculate it, details of the method of calculation are given using data items in the STRUCT_MON_DETAILS category.
Mandatory: no
Keys: _struct_mon_nucl.label_alt_id _struct_mon_nucl.label_asym_id _struct_mon_nucl.label_comp_id _struct_mon_nucl.label_seq_id
Groups: inclusive_group struct_group
Examples:
| Example | Detail |
|---|---|
loop_
_struct_mon_nucl.label_comp_id
_struct_mon_nucl.label_seq_id
_struct_mon_nucl.label_asym_id
_struct_mon_nucl.label_alt_id
_struct_mon_nucl.alpha
_struct_mon_nucl.beta
_struct_mon_nucl.gamma
_struct_mon_nucl.delta
_struct_mon_nucl.epsilon
_struct_mon_nucl.zeta
C 1 A . . . 29.9 131.9 222.1 174.2
G 2 A . 334.0 130.6 33.1 125.6 167.6 270.9
T 3 A . 258.2 178.7 101.0 114.6 216.6 259.3
# ---- abbreviated list -----
|
Example 1 - based on NDB structure BDL028. |
Category: struct_mon_nucl
Mandatory: no
The value in degrees of the backbone torsion angle alpha (O3'-P-O5'-C5').
Type: float
Units: degrees
Mandatory: no
A component of the identifier for participants in the site. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category.
Mandatory: no
A component of the identifier for participants in the site. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category.
Mandatory: no
A component of the identifier for participants in the site. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category.
Category: struct_mon_nucl
Mandatory: no
The value in degrees of the backbone torsion angle beta (P-O5'-C5'-C4').
Type: float
Units: degrees
Category: struct_mon_nucl
Mandatory: no
The value in degrees of the sugar-base torsion angle chi1 (O4'-C1'-N1-C2).
Type: float
Units: degrees
Category: struct_mon_nucl
Mandatory: no
The value in degrees of the sugar-base torsion angle chi2 (O4'-C1'-N9-C4).
Type: float
Units: degrees
Category: struct_mon_nucl
Mandatory: no
The value in degrees of the backbone torsion angle delta (C5'-C4'-C3'-O3').
Type: float
Units: degrees
Category: struct_mon_nucl
Mandatory: no
A description of special aspects of the residue, its conformation, behaviour in refinement, or any other aspect that requires annotation.
Type: float
Example:
Part of the phosphodiester backbone not in
density.
Category: struct_mon_nucl
Mandatory: no
The value in degrees of the backbone torsion angle epsilon (C4'-C3'-O3'-P).
Type: float
Units: degrees
Category: struct_mon_nucl
Mandatory: no
The value in degrees of the backbone torsion angle gamma (O5'-C5'-C4'-C3').
Type: float
Units: degrees
Mandatory: yes
A component of the identifier for participants in the site. This data item is a pointer to _atom_sites_alt.id in the ATOM_SITES_ALT category.
Mandatory: yes
A component of the identifier for participants in the site. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category.
Mandatory: yes
A component of the identifier for participants in the site. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category.
Mandatory: yes
A component of the identifier for participants in the site. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category.
Category: struct_mon_nucl
Mandatory: no
The mean value of the isotropic displacement parameter for all atoms in the monomer.
Type: float
Category: struct_mon_nucl
Mandatory: no
The mean value of the isotropic displacement parameter for atoms in the base moiety of the nucleic acid monomer.
Type: float
Category: struct_mon_nucl
Mandatory: no
The mean value of the isotropic displacement parameter for atoms in the phosphate moiety of the nucleic acid monomer.
Type: float
Category: struct_mon_nucl
Mandatory: no
The mean value of the isotropic displacement parameter for atoms in the sugar moiety of the nucleic acid monomer.
Type: float
Category: struct_mon_nucl
Mandatory: no
The value in degrees of the sugar torsion angle nu0 (C4'-O4'-C1'-C2').
Type: float
Units: degrees
Category: struct_mon_nucl
Mandatory: no
The value in degrees of the sugar torsion angle nu1 (O4'-C1'-C2'-C3').
Type: float
Units: degrees
Category: struct_mon_nucl
Mandatory: no
The value in degrees of the sugar torsion angle nu2 (C1'-C2'-C3'-C4').
Type: float
Units: degrees
Category: struct_mon_nucl
Mandatory: no
The value in degrees of the sugar torsion angle nu3 (C2'-C3'-C4'-O4').
Type: float
Units: degrees
Category: struct_mon_nucl
Mandatory: no
The value in degrees of the sugar torsion angle nu4 (C3'-C4'-O4'-C1').
Type: float
Units: degrees
Category: struct_mon_nucl
Mandatory: no
P is the phase angle of pseudorotation for five-membered rings. For ribose and deoxyribose sugars in nucleic acids (tau4 +tau1)-(tau3+tau0) P = ATAN (-------------------------) 2tau2 (sin 36+sin 72) If tau2 is <0, then P=P+180 degree (Altona & Sundaralingam, 1972). Ref: Altona, C. & Sundaralingam, M. (1972). J. Am. Chem. Soc. 94, 8205-8212.
Type: float
Units: degrees
Category: struct_mon_nucl
Mandatory: no
The real-space (linear) correlation coefficient RSCC, as described by Jones et al. (1991), evaluated over all atoms in the nucleic acid monomer. sum|pobs - <pobs>| * sum|pcalc - <pcalc>| RSCC = ------------------------------------------------- [ sum|pobs - <pobs> |2 * sum|pcalc - <pcalc>|2 ]1/2 pobs = the density in an 'experimental' map pcalc = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in _struct_mon_details.RSCC. < > indicates an average and the sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in _struct_mon_details.RSCC. Ref: Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M. (1991). Acta Cryst. A47, 110-119.
Type: float
Category: struct_mon_nucl
Mandatory: no
The real-space (linear) correlation coefficient RSCC, as described by Jones et al. (1991), evaluated over all atoms in the base moiety of the nucleic acid monomer. sum|pobs - <pobs>| * sum|pcalc - <pcalc>| RSCC = ------------------------------------------------- [ sum|pobs - <pobs> |2 * sum|pcalc - <pcalc>|2 ]1/2 pobs = the density in an 'experimental' map pcalc = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in _struct_mon_details.RSCC. < > indicates an average and the sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in _struct_mon_details.RSCC. Ref: Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M. (1991). Acta Cryst. A47, 110-119.
Type: float
Category: struct_mon_nucl
Mandatory: no
The real-space (linear) correlation coefficient RSCC, as described by Jones et al. (1991), evaluated over all atoms in the phosphate moiety of the nucleic acid monomer. sum|pobs - <pobs>| * sum|pcalc - <pcalc>| RSCC = ------------------------------------------------- [ sum|pobs - <pobs> |2 * sum|pcalc - <pcalc>|2 ]1/2 pobs = the density in an 'experimental' map pcalc = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in _struct_mon_details.RSCC. < > indicates an average and the sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in _struct_mon_details.RSCC. Ref: Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M. (1991). Acta Cryst. A47, 110-119.
Type: float
Category: struct_mon_nucl
Mandatory: no
The real-space (linear) correlation coefficient RSCC, as described by Jones et al. (1991), evaluated over all atoms in the sugar moiety of the nucleic acid monomer. sum|pobs - <pobs>| * sum|pcalc - <pcalc>| RSCC = ------------------------------------------------- [ sum|pobs - <pobs> |2 * sum|pcalc - <pcalc>|2 ]1/2 pobs = the density in an 'experimental' map pcalc = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in _struct_mon_details.RSCC. < > indicates an average and the sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in _struct_mon_details.RSCC. Ref: Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M. (1991). Acta Cryst. A47, 110-119.
Type: float
Category: struct_mon_nucl
Mandatory: no
The real-space residual RSR, as described by Branden & Jones (1990), evaluated over all atoms in the nucleic acid monomer. sum|pobs - pcalc| RSR = --------------------- sum|pobs + pcalc| pobs = the density in an 'experimental' map pcalc = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in _struct_mon_details.RSR. The sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in _struct_mon_details.RSR. Ref: Branden, C.-I. & Jones, T. A. (1990). Nature (London), 343, 687-689.
Type: float
Category: struct_mon_nucl
Mandatory: no
The real-space residual RSR, as described by Branden & Jones (1990), evaluated over all atoms in the base moiety of the nucleic acid monomer. sum|pobs - pcalc| RSR = --------------------- sum|pobs + pcalc| pobs = the density in an 'experimental' map pcalc = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in _struct_mon_details.RSR. The sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in _struct_mon_details.RSR. Ref: Branden, C.-I. & Jones, T. A. (1990). Nature (London), 343, 687-689.
Type: float
Category: struct_mon_nucl
Mandatory: no
The real-space residual RSR, as described by Branden & Jones (1990), evaluated over all atoms in the phosphate moiety of the nucleic acid monomer. sum|pobs - pcalc| RSR = --------------------- sum|pobs + pcalc| pobs = the density in an 'experimental' map pcalc = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in _struct_mon_details.RSR. The sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in _struct_mon_details.RSR. Ref: Branden, C.-I. & Jones, T. A. (1990). Nature (London), 343, 687-689.
Type: float
Category: struct_mon_nucl
Mandatory: no
The real-space residual RSR, as described by Branden & Jones (1990), evaluated over all atoms in the sugar moiety of the nucleic acid monomer. sum|pobs - pcalc| RSR = --------------------- sum|pobs + pcalc| pobs = the density in an 'experimental' map pcalc = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in _struct_mon_details.RSR. The sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in _struct_mon_details.RSR. Ref: Branden, C.-I. & Jones, T. A. (1990). Nature (London), 343, 687-689.
Type: float
Category: struct_mon_nucl
Mandatory: no
The value in degrees of the sugar torsion angle tau0 (C4'-O4'-C1'-C2').
Type: float
Units: degrees
Category: struct_mon_nucl
Mandatory: no
The value in degrees of the sugar torsion angle tau1 (O4'-C1'-C2'-C3').
Type: float
Units: degrees
Category: struct_mon_nucl
Mandatory: no
The value in degrees of the sugar torsion angle tau2 (C1'-C2'-C3'-C4').
Type: float
Units: degrees
Category: struct_mon_nucl
Mandatory: no
The value in degrees of the sugar torsion angle tau3 (C2'-C3'-C4'-O4').
Type: float
Units: degrees
Category: struct_mon_nucl
Mandatory: no
The value in degrees of the sugar torsion angle tau4 (C3'-C4'-O4'-C1').
Type: float
Units: degrees
Category: struct_mon_nucl
Mandatory: no
The maximum amplitude of puckering. This is derived from the pseudorotation value P and the torsion angles in the ribose ring. Tau2= Taum cosP Tau3= Taum cos(P+144) Tau4= Taum cos(P+288) Tau0= Taum cos(P+ 72) Tau1= Taum cos(P+216)
Type: float
Units: degrees
Category: struct_mon_nucl
Mandatory: no
The value in degrees of the backbone torsion angle zeta (C3'-O3'-P-O5').
Type: float
Units: degrees
Data items in the STRUCT_MON_PROT category record details about structural properties of a protein when analyzed at the monomer level. Analogous data items for nucleic acids are given in the STRUCT_MON_NUCL category. For items where the value of the property depends on the method employed to calculate it, details of the method of calculation are given using data items in the STRUCT_MON_DETAILS category.
Mandatory: no
Keys: _struct_mon_prot.label_alt_id _struct_mon_prot.label_asym_id _struct_mon_prot.label_comp_id _struct_mon_prot.label_seq_id
Groups: inclusive_group struct_group
Examples:
| Example | Detail |
|---|---|
_struct_mon_prot.label_comp_id ARG
_struct_mon_prot.label_seq_id 35
_struct_mon_prot.label_asym_id A
_struct_mon_prot.label_alt_id .
_struct_mon_prot.chi1 -67.9
_struct_mon_prot.chi2 -174.7
_struct_mon_prot.chi3 -67.7
_struct_mon_prot.chi4 -86.3
_struct_mon_prot.chi5 4.2
_struct_mon_prot.RSCC_all 0.90
_struct_mon_prot.RSR_all 0.18
_struct_mon_prot.mean_B_all 30.0
_struct_mon_prot.mean_B_main 25.0
_struct_mon_prot.mean_B_side 35.1
_struct_mon_prot.omega 180.1
_struct_mon_prot.phi -60.3
_struct_mon_prot.psi -46.0
|
Example 1 - based on laboratory records for protein NS1. This example provides details for residue ARG 35. |
Category: struct_mon_prot
Mandatory: no
The value in degrees of the side-chain torsion angle chi1, for those residues containing such an angle.
Type: float
Units: degrees
Category: struct_mon_prot
Mandatory: no
The value in degrees of the side-chain torsion angle chi2, for those residues containing such an angle.
Type: float
Units: degrees
Category: struct_mon_prot
Mandatory: no
The value in degrees of the side-chain torsion angle chi3, for those residues containing such an angle.
Type: float
Units: degrees
Category: struct_mon_prot
Mandatory: no
The value in degrees of the side-chain torsion angle chi4, for those residues containing such an angle.
Type: float
Units: degrees
Category: struct_mon_prot
Mandatory: no
The value in degrees of the side-chain torsion angle chi5, for those residues containing such an angle.
Type: float
Units: degrees
Category: struct_mon_prot
Mandatory: no
A description of special aspects of the residue, its conformation, behaviour in refinement, or any other aspect that requires annotation.
Type: float
Examples:
| Example | Detail |
|---|---|
very poor density |
|
The side chain of this density may occupy
alternative conformations, but alternative
conformations were not fit in this model.
|
|
This residue has a close contact with the
bound inhibitor, which may account for
the nonstandard conformation of the side
chain.
|
Mandatory: yes
A component of the identifier for the monomer. This data item is a pointer to _atom_sites_alt.id in the ATOM_SITES_ALT category.
Mandatory: yes
A component of the identifier for the monomer. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category.
Mandatory: yes
A component of the identifier for the monomer. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category.
Mandatory: yes
A component of the identifier for the monomer. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category.
Mandatory: no
A component of the identifier for the monomer. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category.
Mandatory: no
A component of the identifier for the monomer. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category.
Mandatory: no
A component of the identifier for the monomer. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category.
Category: struct_mon_prot
Mandatory: no
The real-space (linear) correlation coefficient RSCC, as described by Jones et al. (1991), evaluated over all atoms in the monomer. sum|pobs - <pobs>| * sum|pcalc - <pcalc>| RSCC = ------------------------------------------------- [ sum|pobs - <pobs> |2 * sum|pcalc - <pcalc>|2 ]1/2 pobs = the density in an 'experimental' map pcalc = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in _struct_mon_details.RSCC. < > indicates an average and the sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in _struct_mon_details.RSCC. Ref: Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M. (1991). Acta Cryst. A47, 110-119.
Type: float
Category: struct_mon_prot
Mandatory: no
The real-space (linear) correlation coefficient RSCC, as described by Jones et al. (1991), evaluated over all atoms in the main chain of the monomer. sum|pobs - <pobs>| * sum|pcalc - <pcalc>| RSCC = ------------------------------------------------- [ sum|pobs - <pobs> |2 * sum|pcalc - <pcalc>|2 ]1/2 pobs = the density in an 'experimental' map pcalc = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in _struct_mon_details.RSCC. < > indicates an average and the sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in _struct_mon_details.RSCC. Ref: Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M. (1991). Acta Cryst. A47, 110-119.
Type: float
Category: struct_mon_prot
Mandatory: no
The real-space (linear) correlation coefficient RSCC, as described by Jones et al. (1991), evaluated over all atoms in the side chain of the monomer. sum|pobs - <pobs>| * sum|pcalc - <pcalc>| RSCC = ------------------------------------------------- [ sum|pobs - <pobs> |2 * sum|pcalc - <pcalc>|2 ]1/2 pobs = the density in an 'experimental' map pcalc = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in _struct_mon_details.RSCC. < > indicates an average and the sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in _struct_mon_details.RSCC. Ref: Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M. (1991). Acta Cryst. A47, 110-119.
Type: float
Category: struct_mon_prot
Mandatory: no
The real-space residual RSR, as described by Branden & Jones (1990), evaluated over all atoms in the monomer. sum|pobs - pcalc| RSR = --------------------- sum|pobs + pcalc| pobs = the density in an 'experimental' map pcalc = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in _struct_mon_details.RSR. The sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in _struct_mon_details.RSR. Ref: Branden, C.-I. & Jones, T. A. (1990). Nature (London), 343, 687-689.
Type: float
Category: struct_mon_prot
Mandatory: no
The real-space residual RSR, as described by Branden & Jones (1990), evaluated over all atoms in the main chain of the monomer. sum|pobs - pcalc| RSR = --------------------- sum|pobs + pcalc| pobs = the density in an 'experimental' map pcalc = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in _struct_mon_details.RSR. The sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in _struct_mon_details.RSR. Ref: Branden, C.-I. & Jones, T. A. (1990). Nature (London), 343, 687-689.
Type: float
Category: struct_mon_prot
Mandatory: no
The real-space residual RSR, as described by Branden & Jones (1990), evaluated over all atoms in the side chain of the monomer. sum|pobs - pcalc| RSR = --------------------- sum|pobs + pcalc| pobs = the density in an 'experimental' map pcalc = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in _struct_mon_details.RSR. The sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in _struct_mon_details.RSR. Ref: Branden, C.-I. & Jones, T. A. (1990). Nature (London), 343, 687-689.
Type: float
Category: struct_mon_prot
Mandatory: no
The mean value of the isotropic displacement parameter for all atoms in the monomer.
Type: float
Category: struct_mon_prot
Mandatory: no
The mean value of the isotropic displacement parameter for atoms in the main chain of the monomer.
Type: float
Category: struct_mon_prot
Mandatory: no
The mean value of the isotropic displacement parameter for atoms in the side chain of the monomer.
Type: float
Category: struct_mon_prot
Mandatory: no
The value in degrees of the main-chain torsion angle omega.
Type: float
Units: degrees
Category: struct_mon_prot
Mandatory: no
The value in degrees of the main-chain torsion angle phi.
Type: float
Units: degrees
Category: struct_mon_prot
Mandatory: no
The value in degrees of the main-chain torsion angle psi.
Type: float
Units: degrees
Data items in the STRUCT_MON_PROT_CIS category identify monomers that have been found to have the peptide bond in the cis conformation. The criterion used to select residues to be designated as containing cis peptide bonds is given in _struct_mon_details.prot_cis.
Mandatory: no
Keys: _struct_mon_prot_cis.label_alt_id _struct_mon_prot_cis.label_asym_id _struct_mon_prot_cis.label_comp_id _struct_mon_prot_cis.label_seq_id
Groups: inclusive_group struct_group
Examples:
| Example | Detail |
|---|---|
loop_
_struct_mon_prot_cis.label_comp_id
_struct_mon_prot_cis.label_seq_id
_struct_mon_prot_cis.label_asym_id
_struct_mon_prot_cis.label_alt_id
PRO 8 L .
PRO 77 L .
PRO 95 L .
PRO 141 L .
# ----- abbreviated -----
|
Example 1 - based on PDB structure 1ACY of Ghiara, Stura, Stanfield, Profy & Wilson [Science (1994), 264, 82-85]. |
Mandatory: yes
A component of the identifier for the monomer. This data item is a pointer to _atom_sites_alt.id in the ATOM_SITES_ALT category.
Mandatory: yes
A component of the identifier for the monomer. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category.
Mandatory: yes
A component of the identifier for the monomer. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category.
Mandatory: yes
A component of the identifier for the monomer. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category.
Mandatory: no
A component of the identifier for the monomer. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category.
Mandatory: no
A component of the identifier for the monomer. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category.
Mandatory: no
A component of the identifier for the monomer. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category.
Data items in the STRUCT_NCS_DOM category record information about the domains in an ensemble of domains related by one or more noncrystallographic symmetry operators. A domain need not correspond to a complete polypeptide chain; it can be composed of one or more segments in a single chain, or by segments from more than one chain.
Mandatory: no
Keys: _struct_ncs_dom.id
Groups: inclusive_group struct_group
Examples:
| Example | Detail |
|---|---|
loop_
_struct_ncs_dom.id
_struct_ncs_dom.details
d1 'Chains A, B, and C'
d2 'Chains D, E, and F'
|
Example 1 - based on laboratory records for the collagen-like peptide, HYP-. |
Category: struct_ncs_dom
Mandatory: no
A description of special aspects of the structural elements that comprise a domain in an ensemble of domains related by noncrystallographic symmetry.
Type: text
Example:
The loop between residues 18 and 23 in this
domain interacts with a symmetry-related
molecule, and thus deviates significantly from
the noncrystallographic threefold.
| Name | Category | Mandatory |
|---|---|---|
| _struct_ncs_dom.id | struct_ncs_dom | yes |
| _struct_ncs_dom_lim.dom_id | struct_ncs_dom_lim | yes |
| _struct_ncs_ens_gen.dom_id_1 | struct_ncs_ens_gen | yes |
| _struct_ncs_ens_gen.dom_id_2 | struct_ncs_ens_gen | yes |
The value of _struct_ncs_dom.id must uniquely identify a record in the STRUCT_NCS_DOM list. Note that this item need not be a number; it can be any unique identifier.
Type: code
Child / Parent relations:
| Child | Parent |
|---|---|
| _struct_ncs_dom_lim.dom_id | _struct_ncs_dom.id |
| _struct_ncs_ens_gen.dom_id_1 | _struct_ncs_dom.id |
| _struct_ncs_ens_gen.dom_id_2 | _struct_ncs_dom.id |
Data items in the STRUCT_NCS_DOM_LIM category identify the start and end points of polypeptide chain segments that form all or part of a domain in an ensemble of domains related by noncrystallographic symmetry.
Mandatory: no
Keys: _struct_ncs_dom_lim.dom_id _struct_ncs_dom_lim.beg_label_alt_id _struct_ncs_dom_lim.beg_label_asym_id _struct_ncs_dom_lim.beg_label_comp_id _struct_ncs_dom_lim.beg_label_seq_id _struct_ncs_dom_lim.end_label_alt_id _struct_ncs_dom_lim.end_label_asym_id _struct_ncs_dom_lim.end_label_comp_id _struct_ncs_dom_lim.end_label_seq_id
Groups: inclusive_group struct_group
Examples:
| Example | Detail |
|---|---|
loop_
_struct_ncs_dom_lim.dom_id
_struct_ncs_dom_lim.beg_label_alt_id
_struct_ncs_dom_lim.beg_label_asym_id
_struct_ncs_dom_lim.beg_label_comp_id
_struct_ncs_dom_lim.beg_label_seq_id
_struct_ncs_dom_lim.end_label_alt_id
_struct_ncs_dom_lim.end_label_asym_id
_struct_ncs_dom_lim.end_label_comp_id
_struct_ncs_dom_lim.end_label_seq_id
d1 . A PRO 1 . A GLY 29
d1 . B PRO 31 . B GLY 59
d1 . C PRO 61 . B GLY 89
d2 . D PRO 91 . D GLY 119
d2 . E PRO 121 . E GLY 149
d2 . F PRO 151 . F GLY 179
|
Example 1 - based on laboratory records for the collagen-like peptide, HYP-. |
Mandatory: yes
A component of the identifier for the monomer at which this segment of the domain begins. This data item is a pointer to _atom_sites_alt.id in the ATOM_SITES_ALT category.
Mandatory: yes
A component of the identifier for the monomer at which this segment of the domain begins. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category.
Mandatory: yes
A component of the identifier for the monomer at which this segment of the domain begins. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category.
Mandatory: yes
A component of the identifier for the monomer at which this segment of the domain begins. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category.
Mandatory: no
A component of the identifier for the monomer at which this segment of the domain begins. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category.
Mandatory: no
A component of the identifier for the monomer at which this segment of the domain begins. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category.
Mandatory: no
A component of the identifier for the monomer at which this segment of the domain begins. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category.
Mandatory: yes
This data item is a pointer to _struct_ncs_dom.id in the STRUCT_NCS_DOM category.
Mandatory: yes
A component of the identifier for the monomer at which this segment of the domain ends. This data item is a pointer to _atom_sites_alt.id in the ATOM_SITES_ALT category.
Mandatory: yes
A component of the identifier for the monomer at which this segment of the domain ends. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category.
Mandatory: yes
A component of the identifier for the monomer at which this segment of the domain ends. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category.
Mandatory: yes
A component of the identifier for the monomer at which this segment of the domain ends. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category.
Mandatory: no
A component of the identifier for the monomer at which this segment of the domain ends. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category.
Mandatory: no
A component of the identifier for the monomer at which this segment of the domain ends. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category.
Mandatory: no
A component of the identifier for the monomer at which this segment of the domain ends. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category.
Data items in the STRUCT_NCS_ENS category record information about ensembles of domains related by noncrystallographic symmetry. The point group of the ensemble when taken as a whole may be specified, as well as any special aspects of the ensemble that require description.
Mandatory: no
Keys: _struct_ncs_ens.id
Groups: inclusive_group struct_group
Examples:
| Example | Detail |
|---|---|
_struct_ncs_ens.id en1
_struct_ncs_ens.details
; The ensemble represents the pseudo-twofold symmetry
between domains d1 and d2.
;
|
Example 1 - based on laboratory records for the collagen-like peptide, HYP-. |
Category: struct_ncs_ens
Mandatory: no
A description of special aspects of the ensemble.
Type: text
Example:
The ensemble has a slight translation between
domains 1 and 4, but overall it can accurately
be described as point group 222
| Name | Category | Mandatory |
|---|---|---|
| _struct_ncs_ens.id | struct_ncs_ens | yes |
| _struct_ncs_ens_gen.ens_id | struct_ncs_ens_gen | yes |
The value of _struct_ncs_ens.id must uniquely identify a record in the STRUCT_NCS_ENS list. Note that this item need not be a number; it can be any unique identifier.
Type: code
Child / Parent relations:
| Child | Parent |
|---|---|
| _struct_ncs_ens_gen.ens_id | _struct_ncs_ens.id |
Category: struct_ncs_ens
Mandatory: no
The point group of the ensemble of structural elements related by one or more noncrystallographic symmetry operations. The relationships need not be precise; this data item is intended to give a rough description of the noncrystallographic symmetry relationships.
Type: line
Examples:
| Example | Detail |
|---|---|
3 |
|
422 |
|
non-proper |
Data items in the STRUCT_NCS_ENS_GEN category list domains related by a noncrystallographic symmetry operation and identify the operator.
Mandatory: no
Keys: _struct_ncs_ens_gen.ens_id _struct_ncs_ens_gen.dom_id_1 _struct_ncs_ens_gen.dom_id_2 _struct_ncs_ens_gen.oper_id
Groups: inclusive_group struct_group
Examples:
| Example | Detail |
|---|---|
_struct_ncs_ens_gen.dom_id_1 d1
_struct_ncs_ens_gen.dom_id_2 d2
_struct_ncs_ens_gen.ens_id en1
_struct_ncs_ens_gen.oper_id ncsop1
|
Example 1 - based on laboratory records for the collagen-like peptide, HYP-. |
Mandatory: yes
The identifier for the domain that will remain unchanged by the transformation operator. This data item is a pointer to _struct_ncs_dom.id in the STRUCT_NCS_DOM category.
Mandatory: yes
The identifier for the domain that will be transformed by application of the transformation operator. This data item is a pointer to _struct_ncs_dom.id in the STRUCT_NCS_DOM category.
Mandatory: yes
This data item is a pointer to _struct_ncs_ens.id in the STRUCT_NCS_ENS category.
Mandatory: yes
This data item is a pointer to _struct_ncs_oper.id in the STRUCT_NCS_OPER category.
Data items in the STRUCT_NCS_OPER category describe the noncrystallographic symmetry operations. Each operator is specified as a matrix and a subsequent translation vector. Operators need not represent proper rotations.
Mandatory: no
Keys: _struct_ncs_oper.id
Groups: inclusive_group struct_group
Examples:
| Example | Detail |
|---|---|
_struct_ncs_oper.id ncsop1
_struct_ncs_oper.code given
_struct_ncs_oper.matrix[1][1] 0.247
_struct_ncs_oper.matrix[1][2] 0.935
_struct_ncs_oper.matrix[1][3] 0.256
_struct_ncs_oper.matrix[2][1] 0.929
_struct_ncs_oper.matrix[2][2] 0.153
_struct_ncs_oper.matrix[2][3] 0.337
_struct_ncs_oper.matrix[3][1] 0.276
_struct_ncs_oper.matrix[3][2] 0.321
_struct_ncs_oper.matrix[3][3] -0.906
_struct_ncs_oper.vector[1] -8.253
_struct_ncs_oper.vector[2] -11.743
_struct_ncs_oper.vector[3] -1.782
_struct_ncs_oper.details
; Matrix and translation vector for pseudo-twofold operation.
;
|
Example 1 - based on laboratory records for the protein NS1. |
Category: struct_ncs_oper
Mandatory: no
A code to indicate whether this operator describes a relationship between coordinates all of which are given in the data block (in which case the value of code is 'given'), or whether the operator is used to generate new coordinates from those that are given in the data block (in which case the value of code is 'generate').
Type: code
Enumeration values:
| Value | Detail |
|---|---|
given |
operator relates coordinates given in the data block |
generate |
operator generates new coordinates from those given in the data block |
Category: struct_ncs_oper
Mandatory: no
A description of special aspects of the noncrystallographic symmetry operator.
Type: text
Example:
The operation is given as a precise threefold
rotation, despite the fact the best rms
fit between domain 1 and domain 2 yields a
rotation of 119.7 degrees and a translation
of 0.13 angstroms.
| Name | Category | Mandatory |
|---|---|---|
| _struct_ncs_oper.id | struct_ncs_oper | yes |
| _struct_ncs_ens_gen.oper_id | struct_ncs_ens_gen | yes |
The value of _struct_ncs_oper.id must uniquely identify a record in the STRUCT_NCS_OPER list. Note that this item need not be a number; it can be any unique identifier.
Type: code
Child / Parent relations:
| Child | Parent |
|---|---|
| _struct_ncs_ens_gen.oper_id | _struct_ncs_oper.id |
Category: struct_ncs_oper
Mandatory: no
Sub-category: matrix
The [1][1] element of the 3x3 matrix component of a noncrystallographic symmetry operation.
Type: float
Category: struct_ncs_oper
Mandatory: no
Sub-category: matrix
The [1][2] element of the 3x3 matrix component of a noncrystallographic symmetry operation.
Type: float
Category: struct_ncs_oper
Mandatory: no
Sub-category: matrix
The [1][3] element of the 3x3 matrix component of a noncrystallographic symmetry operation.
Type: float
Category: struct_ncs_oper
Mandatory: no
Sub-category: matrix
The [2][1] element of the 3x3 matrix component of a noncrystallographic symmetry operation.
Type: float
Category: struct_ncs_oper
Mandatory: no
Sub-category: matrix
The [2][2] element of the 3x3 matrix component of a noncrystallographic symmetry operation.
Type: float
Category: struct_ncs_oper
Mandatory: no
Sub-category: matrix
The [2][3] element of the 3x3 matrix component of a noncrystallographic symmetry operation.
Type: float
Category: struct_ncs_oper
Mandatory: no
Sub-category: matrix
The [3][1] element of the 3x3 matrix component of a noncrystallographic symmetry operation.
Type: float
Category: struct_ncs_oper
Mandatory: no
Sub-category: matrix
The [3][2] element of the 3x3 matrix component of a noncrystallographic symmetry operation.
Type: float
Category: struct_ncs_oper
Mandatory: no
Sub-category: matrix
The [3][3] element of the 3x3 matrix component of a noncrystallographic symmetry operation.
Type: float
Category: struct_ncs_oper
Mandatory: no
Sub-category: vector
The [1] element of the three-element vector component of a noncrystallographic symmetry operation.
Type: float
Category: struct_ncs_oper
Mandatory: no
Sub-category: vector
The [2] element of the three-element vector component of a noncrystallographic symmetry operation.
Type: float
Category: struct_ncs_oper
Mandatory: no
Sub-category: vector
The [3] element of the three-element vector component of a noncrystallographic symmetry operation.
Type: float
Data items in the STRUCT_REF category allow the author of a data block to relate the entities or biological units described in the data block to information archived in external databases. For references to the sequence of a polymer, the value of the data item _struct_ref.seq_align is used to indicate whether the correspondence between the sequence of the entity or biological unit in the data block and the sequence in the referenced database entry is 'complete' or 'partial'. If this value is 'partial', the region (or regions) of the alignment may be delimited using data items in the STRUCT_REF_SEQ category. Similarly, the value of _struct_ref.seq_dif is used to indicate whether the two sequences contain point differences. If the value is 'yes', the differences may be identified and annotated using data items in the STRUCT_REF_SEQ_DIF category.
Mandatory: no
Keys: _struct_ref.id
Groups: inclusive_group struct_group
Examples:
| Example | Detail |
|---|---|
loop_
_struct_ref.id
_struct_ref.entity_id
_struct_ref.biol_id
_struct_ref.db_name
_struct_ref.db_code
_struct_ref.seq_align
_struct_ref.seq_dif
_struct_ref.details
1 1 . 'Genbank' '12345' 'entire' 'yes' .
2 . 2 'PDB' '1ABC' . .
; The structure of the closely related compound,
isobutyryl-pepstatin (pepstatin A) in complex with
rhizopuspepsin
;
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
Mandatory: no
This data item is a pointer to _struct_biol.id in the STRUCT_BIOL category.
Category: struct_ref
Mandatory: yes
The code for this entity or biological unit or for a closely related entity or biological unit in the named database.
Type: line
Examples:
| Example | Detail |
|---|---|
1ABC |
|
ABCDEF |
Category: struct_ref
Mandatory: yes
The name of the database containing reference information about this entity or biological unit.
Type: line
Examples:
| Example | Detail |
|---|---|
PDB |
|
CSD |
|
Genbank |
Category: struct_ref
Mandatory: no
A description of special aspects of the relationship between the entity or biological unit described in the data block and that in the referenced database entry.
Type: text
Mandatory: yes
This data item is a pointer to _entity.id in the ENTITY category.
| Name | Category | Mandatory |
|---|---|---|
| _struct_ref.id | struct_ref | yes |
| _struct_ref_seq.ref_id | struct_ref_seq | yes |
The value of _struct_ref.id must uniquely identify a record in the STRUCT_REF list. Note that this item need not be a number; it can be any unique identifier.
Type: code
Child / Parent relations:
| Child | Parent |
|---|---|
| _struct_ref_seq.ref_id | _struct_ref.id |
Category: struct_ref
Mandatory: no
A flag to indicate the scope of the alignment between the sequence of the entity or biological unit described in the data block and that in the referenced database entry. 'entire' indicates that alignment spans the entire length of both sequences (although point differences may occur and can be annotated using the data items in the STRUCT_REF_SEQ_DIF category). 'partial' indicates a partial alignment. The region (or regions) of the alignment may be delimited using data items in the STRUCT_REF_SEQ category. This data item may also take the value '.', indicating that the reference is not to a sequence.
Type: ucode
Enumeration values:
| Value | Detail |
|---|---|
complete |
alignment is complete |
partial |
alignment is partial |
. |
reference is not to a sequence |
Category: struct_ref
Mandatory: no
A flag to indicate the presence ('yes') or absence ('no') of point differences between the sequence of the entity or biological unit described in the data block and that in the referenced database entry. This data item may also take the value '.', indicating that the reference is not to a sequence.
Type: ucode
Enumeration values:
| Value | Detail |
|---|---|
no |
there are no point differences |
n |
abbreviation for "no" |
yes |
there are point difference |
y |
abbreviation for "yes" |
. |
reference is not to a sequence |
Data items in the STRUCT_REF_SEQ category provide a mechanism for indicating and annotating a region (or regions) of alignment between the sequence of an entity or biological unit described in the data block and the sequence in the referenced database entry.
Mandatory: no
Keys: _struct_ref_seq.align_id
Groups: inclusive_group struct_group
Examples:
| Example | Detail |
|---|---|
_struct_ref_seq.align_id alg1
_struct_ref_seq.ref_id seqdb1
_struct_ref_seq.seq_align_beg 36
_struct_ref_seq.seq_align_end 288
_struct_ref_seq.db_align_beg 18
_struct_ref_seq.db_align_end 276
_struct_ref_seq.details
; The alignment contains 3 gaps larger than 2 residues
;
|
Example 1 - based on the sequence alignment of CHER from M. xantus (36 to 288) and CHER from S. typhimurium (18 to 276). |
| Name | Category | Mandatory |
|---|---|---|
| _struct_ref_seq.align_id | struct_ref_seq | yes |
| _struct_ref_seq_dif.align_id | struct_ref_seq_dif | yes |
The value of _struct_ref_seq.align_id must uniquely identify a record in the STRUCT_REF_SEQ list. Note that this item need not be a number; it can be any unique identifier.
Type: code
Child / Parent relations:
| Child | Parent |
|---|---|
| _struct_ref_seq_dif.align_id | _struct_ref_seq.align_id |
Mandatory: yes
The sequence position in the referenced database entry at which the alignment begins.
Type: int
Mandatory: yes
The sequence position in the referenced database entry at which the alignment ends.
Type: int
Category: struct_ref_seq
Mandatory: no
A description of special aspects of the sequence alignment.
Type: text
Mandatory: yes
This data item is a pointer to _struct_ref.id in the STRUCT_REF category.
Mandatory: yes
The sequence position in the entity or biological unit described in the data block at which the alignment begins. This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category.
Mandatory: yes
The sequence position in the entity or biological unit described in the data block at which the alignment ends. This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category.
Data items in the STRUCT_REF_SEQ_DIF category provide a mechanism for indicating and annotating point differences between the sequence of the entity or biological unit described in the data block and the sequence of the referenced database entry.
Mandatory: no
Keys: _struct_ref_seq_dif.align_id _struct_ref_seq_dif.seq_num
Groups: inclusive_group struct_group
Examples:
| Example | Detail |
|---|---|
_struct_ref_seq_dif.align_id algn2
_struct_ref_seq_dif.seq_num 181
_struct_ref_seq_dif.db_mon_id GLU
_struct_ref_seq_dif.mon_id PHE
_struct_ref_seq_dif.details
; A point mutation was introduced in the CAP at position 181
substituting PHE for GLU.
;
|
Example 1 - based on laboratory records for CAP-DNA complex. |
Mandatory: yes
This data item is a pointer to _struct_ref_seq.align_id in the STRUCT_REF_SEQ category.
Mandatory: yes
The monomer type found at this position in the referenced database entry. This data item is a pointer to _chem_comp.id in the CHEM_COMP category.
Category: struct_ref_seq_dif
Mandatory: no
A description of special aspects of the point differences between the sequence of the entity or biological unit described in the data block and that in the referenced database entry.
Type: text
Mandatory: yes
The monomer type found at this position in the sequence of the entity or biological unit described in this data block. This data item is a pointer to _chem_comp.id in the CHEM_COMP category.
Mandatory: yes
This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category.
Data items in the STRUCT_SHEET category record details about the beta-sheets.
Mandatory: no
Keys: _struct_sheet.id
Groups: inclusive_group struct_group
Examples:
| Example | Detail |
|---|---|
_struct_sheet.id sheet_1
_struct_sheet.type 'beta-barrel'
_struct_sheet.number_strands 8
_struct_sheet.details .
|
Example 1 - simple beta-barrel. N O N O N O N O N O N O 10--11--12--13--14--15--16--17--18--19--20 strand_a N O N O N O N O N O / \ / \ / \ / \ / \ N O N O N O N O N O N O 30--31--32--33--34--35--36--37--38--39--40 strand_b N O N O N O N O N O / \ / \ / \ / \ / \ N O N O N O N O N O N O 50--51--52--53--54--55--56--57--58--59--60 strand_c N O N O N O N O N O / \ / \ / \ / \ / \ N O N O N O N O N O N O 70--71--72--73--74--75--76--77--78--79--80 strand_d N O N O N O N O N O / \ / \ / \ / \ / \ N O N O N O N O N O N O 90--91--92--93--94--95--96--97--98--99-100 strand_e N O N O N O N O N O / \ / \ / \ / \ / \ N O N O N O N O N O N O 110-111-112-113-114-115-116-117-118-119-120 strand_f N O N O N O N O N O / \ / \ / \ / \ / \ N O N O N O N O N O N O 130-131-132-133-134-135-136-137-138-139-140 strand_g N O N O N O N O N O / \ / \ / \ / \ / \ N O N O N O N O N O N O 150-151-152-153-154-155-156-157-158-159-160 strand_h N O N O N O N O N O / \ / \ / \ / \ / \ |
_struct_sheet.id sheet_2
_struct_sheet.type 'five stranded, mixed-sense'
_struct_sheet.number_strands 5
_struct_sheet.details 'strand_d is in two pieces'
|
Example 2 - five stranded mixed-sense sheet with one two-piece strand. N O N O N O N O -10--11--12--13--14--15--16--17--18-> strand_a N O N O N O N O N O | | | | | | | | | | O N O N O N O N O N <-119-118-117-116-115-114-113-112-111-110- strand_b O N O N O N O N O N \ / \ / \ / \ / \ O N O N O N O N O N O N <-41--40--39--38--37--36--35--34--33--32--31--30- strand_c O N O N O N O N O N O N | | | | | | | | | | | | N O N O N O N O N O N O strand_d1 -50--51--52-> -90--91--92--93--95--95--96--97-> strand_d2 N O N O N O N O N O | | | | | | | | | | | | O N O N O N O N O N O N <-80--79--78--77--76--75--74--73--72--71--70- strand_e O N O N O N O N O N |
Category: struct_sheet
Mandatory: no
A description of special aspects of the beta-sheet.
Type: text
| Name | Category | Mandatory |
|---|---|---|
| _struct_sheet.id | struct_sheet | yes |
| _struct_sheet_hbond.sheet_id | struct_sheet_hbond | yes |
| _struct_sheet_order.sheet_id | struct_sheet_order | yes |
| _struct_sheet_range.sheet_id | struct_sheet_range | yes |
| _struct_sheet_topology.sheet_id | struct_sheet_topology | yes |
The value of _struct_sheet.id must uniquely identify a record in the STRUCT_SHEET list. Note that this item need not be a number; it can be any unique identifier.
Type: code
Child / Parent relations:
| Child | Parent |
|---|---|
| _struct_sheet_hbond.sheet_id | _struct_sheet.id |
| _struct_sheet_order.sheet_id | _struct_sheet.id |
| _struct_sheet_range.sheet_id | _struct_sheet.id |
| _struct_sheet_topology.sheet_id | _struct_sheet.id |
Category: struct_sheet
Mandatory: no
The number of strands in the sheet. If a given range of residues bulges out from the strands, it is still counted as one strand. If a strand is composed of two different regions of polypeptide, it is still counted as one strand, as long as the proper hydrogen- bonding connections are made to adjacent strands.
Type: int
Category: struct_sheet
Mandatory: no
A simple descriptor for the type of the sheet.
Type: text
Examples:
| Example | Detail |
|---|---|
jelly-roll |
|
Rossmann fold |
|
beta barrel |
Data items in the STRUCT_SHEET_HBOND category record details about the hydrogen bonding between residue ranges in a beta- sheet. It is necessary to treat hydrogen bonding independently of the designation of ranges, because the hydrogen bonding may begin in different places for the interactions of a given strand with the one preceding it and the one following it in the sheet.
Mandatory: no
Keys: _struct_sheet_hbond.sheet_id _struct_sheet_hbond.range_id_1 _struct_sheet_hbond.range_id_2
Groups: inclusive_group struct_group
Examples:
| Example | Detail |
|---|---|
loop_
_struct_sheet_hbond.sheet_id
_struct_sheet_hbond.range_id_1
_struct_sheet_hbond.range_id_2
_struct_sheet_hbond.range_1_beg_label_seq_id
_struct_sheet_hbond.range_1_beg_label_atom_id
_struct_sheet_hbond.range_2_beg_label_seq_id
_struct_sheet_hbond.range_2_beg_label_atom_id
_struct_sheet_hbond.range_1_end_label_seq_id
_struct_sheet_hbond.range_1_end_label_atom_id
_struct_sheet_hbond.range_2_end_label_seq_id
_struct_sheet_hbond.range_2_end_label_atom_id
sheet_1 strand_a strand_b 11 N 30 O 19 O 40 N
sheet_1 strand_b strand_c 31 N 50 O 39 O 60 N
sheet_1 strand_c strand_d 51 N 70 O 59 O 80 N
sheet_1 strand_d strand_e 71 N 90 O 89 O 100 N
sheet_1 strand_e strand_f 91 N 110 O 99 O 120 N
sheet_1 strand_f strand_g 111 N 130 O 119 O 140 N
sheet_1 strand_g strand_h 131 N 150 O 139 O 160 N
sheet_1 strand_h strand_a 151 N 10 O 159 O 180 N
|
Example 1 - simple beta-barrel. |
loop_
_struct_sheet_hbond.sheet_id
_struct_sheet_hbond.range_id_1
_struct_sheet_hbond.range_id_2
_struct_sheet_hbond.range_1_beg_label_seq_id
_struct_sheet_hbond.range_1_beg_label_atom_id
_struct_sheet_hbond.range_2_beg_label_seq_id
_struct_sheet_hbond.range_2_beg_label_atom_id
_struct_sheet_hbond.range_1_end_label_seq_id
_struct_sheet_hbond.range_1_end_label_atom_id
_struct_sheet_hbond.range_2_end_label_seq_id
_struct_sheet_hbond.range_2_end_label_atom_id
sheet_2 strand_a strand_b 20 N 119 O 18 O 111 N
sheet_2 strand_b strand_c 110 N 33 O 118 N 41 O
sheet_2 strand_c strand_d1 38 N 52 O 40 O 50 N
sheet_2 strand_c strand_d2 30 N 96 O 36 O 90 N
sheet_2 strand_d1 strand_e 51 N 80 O 51 O 80 N
sheet_2 strand_d2 strand_e 91 N 76 O 97 O 70 N
|
Example 2 - five stranded mixed-sense sheet with one two-piece strand. |
Mandatory: yes
A component of the identifier for the residue for the first partner of the first hydrogen bond between two residue ranges in a sheet. This data item is a pointer to _atom_site.label_atom_id in the ATOM_SITE category.
Mandatory: yes
A component of the identifier for the residue for the first partner of the first hydrogen bond between two residue ranges in a sheet. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category.
Mandatory: yes
A component of the identifier for the residue for the first partner of the last hydrogen bond between two residue ranges in a sheet. This data item is a pointer to _atom_site.label_atom_id in the ATOM_SITE category.
Mandatory: yes
A component of the identifier for the residue for the first partner of the last hydrogen bond between two residue ranges in a sheet. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category.
Mandatory: yes
A component of the identifier for the residue for the second partner of the first hydrogen bond between two residue ranges in a sheet. This data item is a pointer to _atom_site.label_atom_id in the ATOM_SITE category.
Mandatory: yes
A component of the identifier for the residue for the second partner of the first hydrogen bond between two residue ranges in a sheet. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category.
Mandatory: yes
A component of the identifier for the residue for the second partner of the last hydrogen bond between two residue ranges in a sheet. This data item is a pointer to _atom_site.label_atom_id in the ATOM_SITE category.
Mandatory: yes
A component of the identifier for the residue for the second partner of the last hydrogen bond between two residue ranges in a sheet. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category.
Mandatory: no
A component of the identifier for the residue for the first partner of the first hydrogen bond between two residue ranges in a sheet. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category.
Mandatory: no
A component of the identifier for the residue for the first partner of the first hydrogen bond between two residue ranges in a sheet. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category.
Mandatory: no
A component of the identifier for the residue for the first partner of the last hydrogen bond between two residue ranges in a sheet. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category.
Mandatory: no
A component of the identifier for the residue for the first partner of the last hydrogen bond between two residue ranges in a sheet. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category.
Mandatory: no
A component of the identifier for the residue for the second partner of the first hydrogen bond between two residue ranges in a sheet. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category.
Mandatory: no
A component of the identifier for the residue for the second partner of the first hydrogen bond between two residue ranges in a sheet. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category.
Mandatory: no
A component of the identifier for the residue for the second partner of the last hydrogen bond between two residue ranges in a sheet. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category.
Mandatory: no
A component of the identifier for the residue for the second partner of the last hydrogen bond between two residue ranges in a sheet. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category.
Mandatory: yes
This data item is a pointer to _struct_sheet_range.id in the STRUCT_SHEET_RANGE category.
Mandatory: yes
This data item is a pointer to _struct_sheet_range.id in the STRUCT_SHEET_RANGE category.
Mandatory: yes
This data item is a pointer to _struct_sheet.id in the STRUCT_SHEET category.
Data items in the STRUCT_SHEET_ORDER category record details about the order of the residue ranges that form a beta-sheet. All order links are pairwise and the specified pairs are assumed to be adjacent to one another in the sheet. These data items are an alternative to the STRUCT_SHEET_TOPOLOGY data items and they allow all manner of sheets to be described.
Mandatory: no
Keys: _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2
Groups: inclusive_group struct_group
Examples:
| Example | Detail |
|---|---|
loop_
_struct_sheet_order.sheet_id
_struct_sheet_order.range_id_1
_struct_sheet_order.range_id_2
_struct_sheet_order.offset
_struct_sheet_order.sense
sheet_1 strand_a strand_b +1 parallel
sheet_1 strand_b strand_c +1 parallel
sheet_1 strand_c strand_d +1 parallel
sheet_1 strand_d strand_e +1 parallel
sheet_1 strand_e strand_f +1 parallel
sheet_1 strand_f strand_g +1 parallel
sheet_1 strand_g strand_h +1 parallel
sheet_1 strand_h strand_a +1 parallel
|
Example 1 - simple beta-barrel. |
loop_
_struct_sheet_order.sheet_id
_struct_sheet_order.range_id_1
_struct_sheet_order.range_id_2
_struct_sheet_order.offset
_struct_sheet_order.sense
sheet_2 strand_a strand_b +1 anti-parallel
sheet_2 strand_b strand_c +1 parallel
sheet_2 strand_c strand_d1 +1 anti-parallel
sheet_2 strand_c strand_d2 +1 anti-parallel
sheet_2 strand_d1 strand_e +1 anti-parallel
sheet_2 strand_d2 strand_e +1 anti-parallel
|
Example 2 - five stranded mixed-sense sheet with one two-piece strand. |
Category: struct_sheet_order
Mandatory: no
Designates the relative position in the sheet, plus or minus, of the second residue range to the first.
Type: int
Mandatory: yes
This data item is a pointer to _struct_sheet_range.id in the STRUCT_SHEET_RANGE category.
Mandatory: yes
This data item is a pointer to _struct_sheet_range.id in the STRUCT_SHEET_RANGE category.
Category: struct_sheet_order
Mandatory: no
A flag to indicate whether the two designated residue ranges are parallel or antiparallel to one another.
Type: ucode
Enumeration values:
| Value | Detail |
|---|---|
parallel |
|
anti-parallel |
Mandatory: yes
This data item is a pointer to _struct_sheet.id in the STRUCT_SHEET category.
Data items in the STRUCT_SHEET_RANGE category record details about the residue ranges that form a beta-sheet. Residues are included in a range if they made beta-sheet-type hydrogen-bonding interactions with at least one adjacent strand and if there are at least two residues in the range.
Mandatory: no
Keys: _struct_sheet_range.sheet_id _struct_sheet_range.id
Groups: inclusive_group struct_group
Examples:
| Example | Detail |
|---|---|
loop_
_struct_sheet_range.sheet_id
_struct_sheet_range.id
_struct_sheet_range.beg_label_comp_id
_struct_sheet_range.beg_label_asym_id
_struct_sheet_range.beg_label_seq_id
_struct_sheet_range.end_label_comp_id
_struct_sheet_range.end_label_asym_id
_struct_sheet_range.end_label_seq_id
_struct_sheet_range.symmetry
sheet_1 strand_a ala A 20 ala A 30 1_555
sheet_1 strand_b ala A 40 ala A 50 1_555
sheet_1 strand_c ala A 60 ala A 70 1_555
sheet_1 strand_d ala A 80 ala A 90 1_555
sheet_1 strand_e ala A 100 ala A 110 1_555
sheet_1 strand_f ala A 120 ala A 130 1_555
sheet_1 strand_g ala A 140 ala A 150 1_555
sheet_1 strand_h ala A 160 ala A 170 1_555
|
Example 1 - simple beta-barrel. |
loop_
_struct_sheet_range.sheet_id
_struct_sheet_range.id
_struct_sheet_range.beg_label_comp_id
_struct_sheet_range.beg_label_asym_id
_struct_sheet_range.beg_label_seq_id
_struct_sheet_range.end_label_comp_id
_struct_sheet_range.end_label_asym_id
_struct_sheet_range.end_label_seq_id
_struct_sheet_range.symmetry
sheet_2 strand_a ala A 10 ala A 18 1_555
sheet_2 strand_b ala A 110 ala A 119 1_555
sheet_2 strand_c ala A 30 ala A 41 1_555
sheet_2 strand_d1 ala A 50 ala A 52 1_555
sheet_2 strand_d2 ala A 90 ala A 97 1_555
sheet_2 strand_e ala A 70 ala A 80 1_555
|
Example 2 - five stranded mixed-sense sheet with one two-piece strand. |
Mandatory: yes
A component of the identifier for the residue at which the beta-sheet range begins. This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category.
Mandatory: yes
A component of the identifier for the residue at which the beta-sheet range begins. This data item is a pointer to _chem_comp.id in the CHEM_COMP category.
Mandatory: yes
A component of the identifier for the residue at which the beta-sheet range begins. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category.
Mandatory: yes
A component of the identifier for the residue at which the beta-sheet range ends. This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category.
Mandatory: yes
A component of the identifier for the residue at which the beta-sheet range ends. This data item is a pointer to _chem_comp.id in the CHEM_COMP category.
Mandatory: yes
A component of the identifier for the residue at which the beta-sheet range ends. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category.
Mandatory: no
A component of the identifier for the residue at which the beta-sheet range begins. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category.
Mandatory: no
A component of the identifier for the residue at which the beta-sheet range begins. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category.
Mandatory: no
A component of the identifier for the residue at which the beta-sheet range begins. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category.
Mandatory: no
A component of the identifier for the residue at which the beta-sheet range ends. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category.
Mandatory: no
A component of the identifier for the residue at which the beta-sheet range ends. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category.
Mandatory: no
A component of the identifier for the residue at which the beta-sheet range ends. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category.
| Name | Category | Mandatory |
|---|---|---|
| _struct_sheet_range.id | struct_sheet_range | yes |
| _struct_sheet_hbond.range_id_1 | struct_sheet_hbond | yes |
| _struct_sheet_hbond.range_id_2 | struct_sheet_hbond | yes |
| _struct_sheet_order.range_id_1 | struct_sheet_order | yes |
| _struct_sheet_order.range_id_2 | struct_sheet_order | yes |
| _struct_sheet_topology.range_id_1 | struct_sheet_topology | yes |
| _struct_sheet_topology.range_id_2 | struct_sheet_topology | yes |
The value of _struct_sheet_range.id must uniquely identify a range in a given sheet in the STRUCT_SHEET_RANGE list. Note that this item need not be a number; it can be any unique identifier.
Type: code
Child / Parent relations:
Mandatory: yes
This data item is a pointer to _struct_sheet.id in the STRUCT_SHEET category.
Category: struct_sheet_range
Mandatory: no
Describes the symmetry operation that should be applied to the residues delimited by the start and end designators in order to generate the appropriate strand in this sheet.
Type: symop
Data items in the STRUCT_SHEET_TOPOLOGY category record details about the topology of the residue ranges that form a beta-sheet. All topology links are pairwise and the specified pairs are assumed to be successive in the amino-acid sequence. These data items are useful in describing various simple and complex folds, but they become inadequate when the strands in the sheet come from more than one chain. The STRUCT_SHEET_ORDER data items can be used to describe single- and multiple-chain-containing sheets.
Mandatory: no
Keys: _struct_sheet_topology.sheet_id _struct_sheet_topology.range_id_1 _struct_sheet_topology.range_id_2
Groups: inclusive_group struct_group
Examples:
| Example | Detail |
|---|---|
loop_
_struct_sheet_topology.sheet_id
_struct_sheet_topology.range_id_1
_struct_sheet_topology.range_id_2
_struct_sheet_topology.offset
_struct_sheet_topology.sense
sheet_1 strand_a strand_b +1 parallel
sheet_1 strand_b strand_c +1 parallel
sheet_1 strand_c strand_d +1 parallel
sheet_1 strand_d strand_e +1 parallel
sheet_1 strand_e strand_f +1 parallel
sheet_1 strand_f strand_g +1 parallel
sheet_1 strand_g strand_h +1 parallel
sheet_1 strand_h strand_a +1 parallel
|
Example 1 - simple beta-barrel. |
loop_
_struct_sheet_topology.sheet_id
_struct_sheet_topology.range_id_1
_struct_sheet_topology.range_id_2
_struct_sheet_topology.offset
_struct_sheet_topology.sense
sheet_2 strand_a strand_c +2 anti-parallel
sheet_2 strand_c strand_d1 +1 anti-parallel
sheet_2 strand_d1 strand_e +1 anti-parallel
sheet_2 strand_e strand_d2 -1 anti-parallel
sheet_2 strand_d2 strand_b -2 anti-parallel
|
Example 2 - five stranded mixed-sense sheet with one two-piece strand. |
Category: struct_sheet_topology
Mandatory: no
Designates the relative position in the sheet, plus or minus, of the second residue range to the first.
Type: int
Mandatory: yes
This data item is a pointer to _struct_sheet_range.id in the STRUCT_SHEET_RANGE category.
Mandatory: yes
This data item is a pointer to _struct_sheet_range.id in the STRUCT_SHEET_RANGE category.
Category: struct_sheet_topology
Mandatory: no
A flag to indicate whether the two designated residue ranges are parallel or antiparallel to one another.
Type: ucode
Enumeration values:
| Value | Detail |
|---|---|
parallel |
|
anti-parallel |
Mandatory: yes
This data item is a pointer to _struct_sheet.id in the STRUCT_SHEET category.
Data items in the STRUCT_SITE category record details about portions of the structure that contribute to structurally relevant sites (e.g. active sites, substrate-binding subsites, metal-coordination sites).
Mandatory: no
Keys: _struct_site.id
Groups: inclusive_group struct_group
Examples:
| Example | Detail |
|---|---|
loop_
_struct_site.id
_struct_site.details
'P2 site C'
; residues with a contact < 3.7 \%A to an atom in the P2
moiety of the inhibitor in the conformation with
_struct_asym.id = C
;
'P2 site D'
; residues with a contact < 3.7 \%A to an atom in the P1
moiety of the inhibitor in the conformation with
_struct_asym.id = D)
;
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
Category: struct_site
Mandatory: no
A description of special aspects of the site.
Type: text
| Name | Category | Mandatory |
|---|---|---|
| _struct_site.id | struct_site | yes |
| _struct_site_gen.site_id | struct_site_gen | yes |
| _struct_site_keywords.site_id | struct_site_keywords | yes |
| _struct_site_view.site_id | struct_site_view | yes |
The value of _struct_site.id must uniquely identify a record in the STRUCT_SITE list. Note that this item need not be a number; it can be any unique identifier.
Type: line
Child / Parent relations:
| Child | Parent |
|---|---|
| _struct_site_gen.site_id | _struct_site.id |
| _struct_site_keywords.site_id | _struct_site.id |
| _struct_site_view.site_id | _struct_site.id |
Data items in the STRUCT_SITE_GEN category record details about the generation of portions of the structure that contribute to structurally relevant sites.
Mandatory: no
Keys: _struct_site_gen.id _struct_site_gen.site_id
Groups: inclusive_group struct_group
Examples:
| Example | Detail |
|---|---|
loop_
_struct_site_gen.id
_struct_site_gen.site_id
_struct_site_gen.label_comp_id
_struct_site_gen.label_asym_id
_struct_site_gen.label_seq_id
_struct_site_gen.symmetry
_struct_site_gen.details
1 1 VAL A 32 1_555 .
2 1 ILE A 47 1_555 .
3 1 VAL A 82 1_555 .
4 1 ILE A 84 1_555 .
5 2 VAL B 232 1_555 .
6 2 ILE B 247 1_555 .
7 2 VAL B 282 1_555 .
8 2 ILE B 284 1_555 .
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
Category: struct_site_gen
Mandatory: no
A description of special aspects of the symmetry generation of this portion of the structural site.
Type: text
Example:
The zinc atom lies on a special position;
application of symmetry elements to generate
the insulin hexamer will generate excess zinc
atoms, which must be removed by hand.
Category: struct_site_gen
Mandatory: yes
The value of _struct_site_gen.id must uniquely identify a record in the STRUCT_SITE_GEN list. Note that this item need not be a number; it can be any unique identifier.
Type: line
Mandatory: yes
A component of the identifier for participants in the site. This data item is a pointer to _atom_sites_alt.id in the ATOM_SITES_ALT category.
Mandatory: yes
A component of the identifier for participants in the site. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category.
Mandatory: yes
A component of the identifier for participants in the site. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category.
Mandatory: yes
A component of the identifier for participants in the site. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category.
Mandatory: yes
A component of the identifier for participants in the site. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category.
Mandatory: no
A component of the identifier for participants in the site. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category.
Mandatory: no
A component of the identifier for participants in the site. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category.
Mandatory: no
A component of the identifier for participants in the site. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category.
Mandatory: no
A component of the identifier for participants in the site. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category.
Mandatory: yes
This data item is a pointer to _struct_site.id in the STRUCT_SITE category.
Category: struct_site_gen
Mandatory: no
Describes the symmetry operation that should be applied to the atom set specified by _struct_site_gen.label* to generate a portion of the site.
Type: symop
Examples:
| Example | Detail |
|---|---|
. |
no symmetry or translation to site |
4 |
4th symmetry operation applied |
7_645 |
7th symm. posn.; +a on x; -b on y |
Data items in the STRUCT_SITE_KEYWORDS category record keywords describing the site.
Mandatory: no
Keys: _struct_site_keywords.site_id _struct_site_keywords.text
Groups: inclusive_group struct_group
Examples:
| Example | Detail |
|---|---|
loop_
_struct_site_keywords.site_id
_struct_site_keywords.text
'P2 site C' 'binding site'
'P2 site C' 'binding pocket'
'P2 site C' 'P2 site'
'P2 site C' 'P2 pocket'
'P2 site D' 'binding site'
'P2 site D' 'binding pocket'
'P2 site D' 'P2 site'
'P2 site D' 'P2 pocket'
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
Mandatory: yes
This data item is a pointer to _struct_site.id in the STRUCT_SITE category.
Category: struct_site_keywords
Mandatory: yes
Keywords describing this site.
Type: text
Examples:
| Example | Detail |
|---|---|
active site |
|
binding pocket |
|
Ca coordination |
Data items in the STRUCT_SITE_VIEW category record details about how to draw and annotate an informative view of the site.
Mandatory: no
Keys: _struct_site_view.id
Groups: inclusive_group struct_group
Examples:
| Example | Detail |
|---|---|
_struct_site_view.id 1
_struct_site_view.rot_matrix[1][1] 0.132
_struct_site_view.rot_matrix[1][2] 0.922
_struct_site_view.rot_matrix[1][3] -0.363
_struct_site_view.rot_matrix[2][1] 0.131
_struct_site_view.rot_matrix[2][2] -0.380
_struct_site_view.rot_matrix[2][3] -0.916
_struct_site_view.rot_matrix[3][1] -0.982
_struct_site_view.rot_matrix[3][2] 0.073
_struct_site_view.rot_matrix[3][3] -0.172
_struct_site_view.details
; This view highlights the site of ATAT-Netropsin
interaction.
;
|
Example 1 - based on NDB structure GDL001 by Coll, Aymami, Van Der Marel, Van Boom, Rich & Wang [Biochemistry (1989), 28, 310-320]. |
Category: struct_site_view
Mandatory: no
A description of special aspects of this view of the site. This data item can be used as a figure legend.
Type: text
Example:
The active site has been oriented with the
specificity pocket on the right and the active
site machinery on the left.
Category: struct_site_view
Mandatory: yes
The value of _struct_site_view.id must uniquely identify a record in the STRUCT_SITE_VIEW list. Note that this item need not be a number; it can be any unique identifier.
Type: line
Examples:
| Example | Detail |
|---|---|
Figure 1 |
|
unliganded enzyme |
|
view down enzyme active site |
Category: struct_site_view
Mandatory: no
Sub-category: matrix
The [1][1] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_SITE_GEN category to an orientation useful for visualizing the site. The conventions used in the rotation are described in _struct_site_view.details. |x'| |11 12 13| |x| |y'|reoriented Cartesian = |21 22 23| |y|Cartesian |z'| |31 32 33| |z|
Type: float
Category: struct_site_view
Mandatory: no
Sub-category: matrix
The [1][2] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_SITE_GEN category to an orientation useful for visualizing the site. The conventions used in the rotation are described in _struct_site_view.details. |x'| |11 12 13| |x| |y'|reoriented Cartesian = |21 22 23| |y|Cartesian |z'| |31 32 33| |z|
Type: float
Category: struct_site_view
Mandatory: no
Sub-category: matrix
The [1][3] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_SITE_GEN category to an orientation useful for visualizing the site. The conventions used in the rotation are described in _struct_site_view.details. |x'| |11 12 13| |x| |y'|reoriented Cartesian = |21 22 23| |y|Cartesian |z'| |31 32 33| |z|
Type: float
Category: struct_site_view
Mandatory: no
Sub-category: matrix
The [2][1] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_SITE_GEN category to an orientation useful for visualizing the site. The conventions used in the rotation are described in _struct_site_view.details. |x'| |11 12 13| |x| |y'|reoriented Cartesian = |21 22 23| |y|Cartesian |z'| |31 32 33| |z|
Type: float
Category: struct_site_view
Mandatory: no
Sub-category: matrix
The [2][2] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_SITE_GEN category to an orientation useful for visualizing the site. The conventions used in the rotation are described in _struct_site_view.details. |x'| |11 12 13| |x| |y'|reoriented Cartesian = |21 22 23| |y|Cartesian |z'| |31 32 33| |z|
Type: float
Category: struct_site_view
Mandatory: no
Sub-category: matrix
The [2][3] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_SITE_GEN category to an orientation useful for visualizing the site. The conventions used in the rotation are described in _struct_site_view.details. |x'| |11 12 13| |x| |y'|reoriented Cartesian = |21 22 23| |y|Cartesian |z'| |31 32 33| |z|
Type: float
Category: struct_site_view
Mandatory: no
Sub-category: matrix
The [3][1] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_SITE_GEN category to an orientation useful for visualizing the site. The conventions used in the rotation are described in _struct_site_view.details. |x'| |11 12 13| |x| |y'|reoriented Cartesian = |21 22 23| |y|Cartesian |z'| |31 32 33| |z|
Type: float
Category: struct_site_view
Mandatory: no
Sub-category: matrix
The [3][2] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_SITE_GEN category to an orientation useful for visualizing the site. The conventions used in the rotation are described in _struct_site_view.details. |x'| |11 12 13| |x| |y'|reoriented Cartesian = |21 22 23| |y|Cartesian |z'| |31 32 33| |z|
Type: float
Category: struct_site_view
Mandatory: no
Sub-category: matrix
The [3][3] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_SITE_GEN category an orientation useful for visualizing the site. The conventions used in the rotation are described in _struct_site_view.details. |x'| |11 12 13| |x| |y'|reoriented Cartesian = |21 22 23| |y|Cartesian |z'| |31 32 33| |z|
Type: float
Mandatory: yes
This data item is a pointer to _struct_site.id in the STRUCT_SITE category.
Data items in the SYMMETRY category record details about the space-group symmetry.
Mandatory: no
Keys: _symmetry.entry_id
Groups: inclusive_group symmetry_group
Examples:
| Example | Detail |
|---|---|
_symmetry.entry_id '5HVP'
_symmetry.cell_setting orthorhombic
_symmetry.Int_Tables_number 18
_symmetry.space_group_name_H-M 'P 21 21 2'
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
Mandatory: yes
This data item is a pointer to _entry.id in the ENTRY category.
Category: symmetry
Mandatory: no
The cell settings for this space-group symmetry.
Alias: _symmetry_cell_setting (cif_core.dic, 2.0.1)
Type: ucode
Enumeration values:
| Value | Detail |
|---|---|
triclinic |
|
monoclinic |
|
orthorhombic |
|
tetragonal |
|
rhombohedral |
|
trigonal |
|
hexagonal |
|
cubic |
Category: symmetry
Mandatory: no
Space-group number from International Tables for Crystallography Vol. A (2002).
Alias: _symmetry_Int_Tables_number (cif_core.dic, 2.0.1)
Type: int
Category: symmetry
Mandatory: no
Space-group symbol as described by Hall (1981). This symbol gives the space-group setting explicitly. Leave spaces between the separate components of the symbol. Ref: Hall, S. R. (1981). Acta Cryst. A37, 517-525; erratum (1981) A37, 921.
Alias: _symmetry_space_group_name_Hall (cif_core.dic, 2.0.1)
Type: line
Examples:
| Example | Detail |
|---|---|
-P 2ac 2n |
|
-R 3 2" |
|
P 61 2 2 (0 0 -1) |
Category: symmetry
Mandatory: no
Hermann-Mauguin space-group symbol. Note that the Hermann-Mauguin symbol does not necessarily contain complete information about the symmetry and the space-group origin. If used, always supply the FULL symbol from International Tables for Crystallography Vol. A (2002) and indicate the origin and the setting if it is not implicit. If there is any doubt that the equivalent positions can be uniquely deduced from this symbol, specify the _symmetry_equiv.pos_as_xyz or _symmetry.space_group_name_Hall data items as well. Leave spaces between symbols referring to different axes.
Alias: _symmetry_space_group_name_H-M (cif_core.dic, 2.0.1)
Type: line
Examples:
| Example | Detail |
|---|---|
P 1 21/m 1 |
|
P 2/n 2/n 2/n (origin at -1) |
|
R -3 2/m |
Data items in the SYMMETRY_EQUIV category list the symmetry-equivalent positions for the space group.
Mandatory: no
Keys: _symmetry_equiv.id
Groups: inclusive_group symmetry_group
Examples:
| Example | Detail |
|---|---|
loop_
_symmetry_equiv.id
_symmetry_equiv.pos_as_xyz
1 '+x,+y,+z'
2 '-x,-y,z'
3 '1/2+x,1/2-y,-z'
4 '1/2-x,1/2+y,-z'
|
Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. |
Category: symmetry_equiv
Mandatory: yes
The value of _symmetry_equiv.id must uniquely identify a record in the SYMMETRY_EQUIV category. Note that this item need not be a number; it can be any unique identifier.
Alias: _symmetry_equiv_pos_site_id (cif_core.dic, 2.0.1)
Type: code
Category: symmetry_equiv
Mandatory: no
Symmetry-equivalent position in the 'xyz' representation. Except for the space group P1, these data will be repeated in a loop. The format of the data item is as per International Tables for Crystallography Vol. A (2002). All equivalent positions should be entered, including those for lattice centring and a centre of symmetry, if present.
Alias: _symmetry_equiv_pos_as_xyz (cif_core.dic, 2.0.1)
Type: line
Example:
-y+x,-y,1/3+z
Category: atom_site
Mandatory: no
A standard code used to describe the type of atomic displacement parameters used for the site.
Related items: _atom_site_adp_type (cif_core.dic, 2.3)
Type: code
Related item: _atom_site.thermal_displace_type (alternate)
Enumeration values:
| Value | Detail |
|---|---|
Uani |
anisotropic Uij |
Uiso |
isotropic U |
Uovl |
overall U |
Umpe |
multipole expansion U |
Bani |
anisotropic Bij |
Biso |
isotropic B |
Bovl |
overall B |
Category: atom_site
Mandatory: no
A concatenated series of single-letter codes which indicate the refinement restraints or constraints applied to this site. This item should not be used. It has been replaced by _atom_site.refinement_flags_posn, *_adp and *_occupancy. It is retained in this dictionary only to provide compatibility with old CIFs.
Related items: _atom_site_refinement_flags (cif_core.dic, 2.3)
Type: code
Related items: _atom_site.refinement_flags_posn (replaces) _atom_site.refinement_flags_adp (replaces) _atom_site.refinement_flags_occupancy (replaces)
Enumeration values:
| Value | Detail |
|---|---|
. |
no refinement constraints |
S |
special-position constraint on site |
G |
rigid-group refinement of site |
R |
riding-atom site attached to non-riding atom |
D |
distance or angle restraint on site |
T |
thermal displacement constraints |
U |
Uiso or Uij restraint (rigid bond) |
P |
partial occupancy constraint |
Category: atom_site
Mandatory: no
A code which indicates the refinement restraints or constraints applied to the atomic displacement parameters of this site.
Related items: _atom_site_refinement_flags_adp (cif_core.dic, 2.3)
Type: code
Related item: _atom_site.refinement_flags_posn (alternate)
Enumeration values:
| Value | Detail |
|---|---|
. |
no constraints on atomic displacement parameters |
T |
special-position constraints on atomic displacement parameters |
U |
Uiso or Uij restraint (rigid bond) |
TU |
both constraints applied |
Category: atom_site
Mandatory: no
A code which indicates that refinement restraints or constraints were applied to the occupancy of this site.
Related items: _atom_site_refinement_flags_occupancy (cif_core.dic, 2.3)
Type: code
Related item: _atom_site.refinement_flags_posn (alternate)
Enumeration values:
| Value | Detail |
|---|---|
. |
no constraints on site-occupancy parameters |
P |
site-occupancy constraint |
Category: atom_site
Mandatory: no
A code which indicates the refinement restraints or constraints applied to the positional coordinates of this site.
Related items: _atom_site_refinement_flags_posn (cif_core.dic, 2.3)
Type: code
Related item: _atom_site.refinement_flags_posn (alternate)
Enumeration values:
| Value | Detail |
|---|---|
. |
no constraints on positional coordinates |
D |
distance or angle restraint on positional coordinates |
G |
rigid-group refinement of positional coordinates |
R |
riding-atom site attached to non-riding atom |
S |
special-position constraint on positional coordinates |
DG |
combination of the above constraints |
DR |
combination of the above constraints |
DS |
combination of the above constraints |
GR |
combination of the above constraints |
GS |
combination of the above constraints |
RS |
combination of the above constraints |
DGR |
combination of the above constraints |
DGS |
combination of the above constraints |
DRS |
combination of the above constraints |
GRS |
combination of the above constraints |
DGRS |
combination of the above constraints |
Category: atom_sites
Mandatory: no
Additional information about the atomic coordinates not coded elsewhere in the CIF.
Related items: _atom_sites_special_details (cif_core.dic, 2.3)
Type: text
Category: atom_type
Mandatory: no
Reference to the source of the real and imaginary dispersion corrections for scattering factors used for this atom type.
Related items: _atom_type_scat_dispersion_source (cif_core.dic, 2.3)
Type: text
Example:
International Tables Vol. IV Table 2.3.1
Data items in the AUDIT_LINK category record details about the relationships between data blocks in the current CIF.
Mandatory: no
Keys: _audit_link.block_code _audit_link.block_description
Examples:
| Example | Detail |
|---|---|
loop_
_audit_link.block_code
_audit_link.block_description
. 'discursive text of paper with two structures'
morA_(1) 'structure 1 of 2'
morA_(2) 'structure 2 of 2'
|
Example 1 - multiple structure paper, as illustrated in A Guide to CIF for Authors (1995). IUCr: Chester. |
loop_
_audit_link.block_code
_audit_link.block_description
. 'publication details'
KSE_COM 'experimental data common to ref./mod. structures'
KSE_REF 'reference structure'
KSE_MOD 'modulated structure'
|
Example 2 - example file for the one-dimensional incommensurately modulated structure of K~2~SeO~4~. |
Category: audit_link
Mandatory: yes
The value of _audit_block.code associated with a data block in the current file related to the current data block. The special value '.' may be used to refer to the current data block for completeness.
Related items: _audit_link_block_code (cif_core.dic, 2.3)
Type: code
Category: audit_link
Mandatory: yes
A textual description of the relationship of the referenced data block to the current one.
Related items: _audit_link_block_description (cif_core.dic, 2.3)
Type: text
Category: cell
Mandatory: no
The angle (recip-alpha) defining the reciprocal cell in degrees. (recip-alpha), (recip-alpha) and (recip-alpha) related to the angles in the real cell by: cos(recip-alpha) = [cos(beta)*cos(gamma) - cos(alpha)]/[sin(beta)*sin(gamma)] cos(recip-beta) = [cos(gamma)*cos(alpha) - cos(beta)]/[sin(gamma)*sin(alpha)] cos(recip-gamma) = [cos(alpha)*cos(beta) - cos(gamma)]/[sin(alpha)*sin(beta)] Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360. New York: John Wiley & Sons Inc.
Related items: _cell_reciprocal_angle_alpha (cif_core.dic, 2.3)
Type: float
Type conditions: esd
Units: degrees
Related item: _cell.reciprocal_angle_alpha_esd (associated_esd)
Default value: 90.0
Range: [0.0, 0.0] [0.0, 180.0] [180.0, 180.0]
Category: cell
Mandatory: no
The angle (recip-beta) defining the reciprocal cell in degrees. (recip-alpha), (recip-alpha) and (recip-alpha) related to the angles in the real cell by: cos(recip-alpha) = [cos(beta)*cos(gamma) - cos(alpha)]/[sin(beta)*sin(gamma)] cos(recip-beta) = [cos(gamma)*cos(alpha) - cos(beta)]/[sin(gamma)*sin(alpha)] cos(recip-gamma) = [cos(alpha)*cos(beta) - cos(gamma)]/[sin(alpha)*sin(beta)] Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360. New York: John Wiley & Sons Inc.
Related items: _cell_reciprocal_angle_beta (cif_core.dic, 2.3)
Type: float
Type conditions: esd
Units: degrees
Related item: _cell.reciprocal_angle_beta_esd (associated_esd)
Default value: 90.0
Range: [0.0, 0.0] [0.0, 180.0] [180.0, 180.0]
Category: cell
Mandatory: no
The angle (recip-gamma) defining the reciprocal cell in degrees. (recip-alpha), (recip-alpha) and (recip-alpha) related to the angles in the real cell by: cos(recip-alpha) = [cos(beta)*cos(gamma) - cos(alpha)]/[sin(beta)*sin(gamma)] cos(recip-beta) = [cos(gamma)*cos(alpha) - cos(beta)]/[sin(gamma)*sin(alpha)] cos(recip-gamma) = [cos(alpha)*cos(beta) - cos(gamma)]/[sin(alpha)*sin(beta)] Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360. New York: John Wiley & Sons Inc.
Related items: _cell_reciprocal_angle_gamma (cif_core.dic, 2.3)
Type: float
Type conditions: esd
Units: degrees
Related item: _cell.reciprocal_angle_gamma_esd (associated_esd)
Default value: 90.0
Range: [0.0, 0.0] [0.0, 180.0] [180.0, 180.0]
Category: cell
Mandatory: no
The estimated standard deviation of _cell.reciprocal_angle_alpha.
Type: float
Units: degrees
Related item: _cell.reciprocal_angle_alpha (associated_value)
Category: cell
Mandatory: no
The estimated standard deviation of _cell.reciprocal_angle_beta.
Type: float
Units: degrees
Related item: _cell.reciprocal_angle_beta (associated_value)
Category: cell
Mandatory: no
The estimated standard deviation of _cell.reciprocal_angle_gamma.
Type: float
Units: degrees
Related item: _cell.reciprocal_angle_gamma (associated_value)
Category: cell
Mandatory: no
The reciprocal cell length (recip-a) in inverse Angstroms. (recip-a), (recip-b) and (recip-c) are related to the real cell by the following equation: recip-a = b*c*sin(alpha)/V recip-b = c*a*sin(beta)/V recip-c = a*b*sin(gamma)/V where V is the cell volume. Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360. New York: John Wiley & Sons Inc.
Related items: _cell_reciprocal_length_a (cif_core.dic, 2.3)
Type: float
Type conditions: esd
Units: reciprocal_angstroms
Related item: _cell.reciprocal_length_a_esd (associated_esd)
Range: [0.0, 0.0] [0.0, .]
Category: cell
Mandatory: no
The reciprocal cell length (recip-b) in inverse Angstroms. (recip-a), (recip-b) and (recip-c) are related to the real cell by the following equation: recip-a = b*c*sin(alpha)/V recip-b = c*a*sin(beta)/V recip-c = a*b*sin(gamma)/V where V is the cell volume. Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360. New York: John Wiley & Sons Inc.
Related items: _cell_reciprocal_length_b (cif_core.dic, 2.3)
Type: float
Type conditions: esd
Units: reciprocal_angstroms
Related item: _cell.reciprocal_length_b_esd (associated_esd)
Range: [0.0, 0.0] [0.0, .]
Category: cell
Mandatory: no
The reciprocal cell length (recip-c) in inverse Angstroms. (recip-a), (recip-b) and (recip-c) are related to the real cell by the following equation: recip-a = b*c*sin(alpha)/V recip-b = c*a*sin(beta)/V recip-c = a*b*sin(gamma)/V where V is the cell volume. Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360. New York: John Wiley & Sons Inc.
Related items: _cell_reciprocal_length_c (cif_core.dic, 2.3)
Type: float
Type conditions: esd
Units: reciprocal_angstroms
Related item: _cell.reciprocal_length_c_esd (associated_esd)
Range: [0.0, 0.0] [0.0, .]
Category: cell
Mandatory: no
The estimated standard deviation of _cell.reciprocal_length_a.
Type: float
Units: reciprocal_angstroms
Related item: _cell.reciprocal_length_a (associated_value)
Category: cell
Mandatory: no
The estimated standard deviation of _cell.reciprocal_length_b.
Type: float
Units: reciprocal_angstroms
Related item: _cell.reciprocal_length_b (associated_value)
Category: cell
Mandatory: no
The estimated standard deviation of _cell.reciprocal_length_c.
Type: float
Units: reciprocal_angstroms
Related item: _cell.reciprocal_length_c (associated_value)
Category: chemical
Mandatory: no
Necessary conditions for the assignment of _chemical.absolute_configuration are given by H. D. Flack and G. Bernardinelli (1999, 2000). Ref: Flack, H. D. & Bernardinelli, G. (1999). Acta Cryst. A55, 908-915. (http://www.iucr.org/paper?sh0129) Flack, H. D. & Bernardinelli, G. (2000). J. Appl. Cryst. 33, 1143-1148. (http://www.iucr.org/paper?ks0021)
Related items: _chemical_absolute_configuration (cif_core.dic, 2.3)
Type: code
Enumeration values:
| Value | Detail |
|---|---|
rm |
absolute configuration established by the structure determination of a compound containing a chiral reference molecule of known absolute configuration |
ad |
absolute configuration established by anomalous-dispersion effects in diffraction measurements on the crystal |
rmad |
absolute configuration established by the structure determination of a compound containing a chiral reference molecule of known absolute configuration and confirmed by anomalous-dispersion effects in diffraction measurements on the crystal |
syn |
absolute configuration has not been established by anomalous-dispersion effects in diffraction measurements on the crystal. The enantiomer has been assigned by reference to an unchanging chiral centre in the synthetic procedure |
unk |
absolute configuration is unknown, there being no firm chemical evidence for its assignment to hand and it having not been established by anomalous-dispersion effects in diffraction measurements on the crystal. An arbitrary choice of enantiomer has been made |
. |
inapplicable |
Category: chemical
Mandatory: no
A temperature in kelvins above which the melting point (the temperature at which the crystalline solid changes to a liquid) lies. _chemical.melting_point_gt and _chemical.melting_point_lt allow a range of temperatures to be given. _chemical.melting_point should always be used in preference to these two items whenever possible.
Related items: _chemical_melting_point_gt (cif_core.dic, 2.3)
Type: float
Units: kelvins
Related item: _chemical.melting_point (alternate)
Range: [0.0, 0.0] [0.0, .]
Category: chemical
Mandatory: no
A temperature in kelvins below which the melting point (the temperature at which the crystalline solid changes to a liquid) lies. _chemical.melting_point_gt and _chemical.melting_point_lt allow a range of temperatures to be given. _chemical.melting_point should always be used in preference to these two items whenever possible.
Related items: _chemical_melting_point_lt (cif_core.dic, 2.3)
Type: float
Units: kelvins
Related item: _chemical.melting_point (alternate)
Range: [0.0, 0.0] [0.0, .]
Category: chemical
Mandatory: no
The optical rotation in solution of the compound is specified in the following format: '[α]TEMPWAVE = SORT (c = CONC, SOLV)' where: TEMP is the temperature of the measurement in degrees Celsius, WAVE is an indication of the wavelength of the light used for the measurement, CONC is the concentration of the solution given as the mass of the substance in g in 100 ml of solution, SORT is the signed value (preceded by a + or a - sign) of 100.α/(l.c), where α is the signed optical rotation in degrees measured in a cell of length l in dm and c is the value of CONC as defined above, and SOLV is the chemical formula of the solvent.
Related items: _chemical_optical_rotation (cif_core.dic, 2.3)
Type: line
Example:
[\a]^25^~D~ = +108 (c = 3.42, CHCl~3~)
Category: chemical
Mandatory: no
A free-text description of the biological properties of the material.
Related items: _chemical_properties_biological (cif_core.dic, 2.3)
Type: text
Examples:
| Example | Detail |
|---|---|
diverse biological activities including use as a
laxative and strong antibacterial activity against
S. aureus and weak activity against
cyclooxygenase-1 (COX-1)
|
|
antibiotic activity against Bacillus subtilis
(ATCC 6051) but no significant activity against
Candida albicans (ATCC 14053), Aspergillus flavus
(NRRL 6541) and Fusarium verticillioides (NRRL
25457)
|
|
weakly potent lipoxygenase nonredox inhibitor
|
|
no influenza A virus sialidase inhibitory and
plaque reduction activities
|
|
low toxicity against Drosophila melanogaster
|
Category: chemical
Mandatory: no
A free-text description of the physical properties of the material.
Related items: _chemical_properties_physical (cif_core.dic, 2.3)
Type: text
Examples:
| Example | Detail |
|---|---|
air-sensitive |
|
moisture-sensitive |
|
hygroscopic |
|
deliquescent |
|
oxygen-sensitive |
|
photo-sensitive |
|
pyrophoric |
|
semiconductor |
|
ferromagnetic at low temperature |
|
paramagnetic and thermochromic |
Category: chemical
Mandatory: no
The temperature in kelvins at which the solid decomposes.
Related items: _chemical_temperature_decomposition (cif_core.dic, 2.3)
Type: float
Type conditions: esd
Units: kelvins
Related item: _chemical.temperature_decomposition_esd (associated_esd)
Range: [0.0, 0.0] [0.0, .]
Example:
350
Category: chemical
Mandatory: no
The estimated standard deviation of _chemical.temperature_decomposition.
Type: float
Units: kelvins
Related item: _chemical.temperature_decomposition (associated_value)
Category: chemical
Mandatory: no
A temperature in kelvins above which the solid is known to decompose. _chemical.temperature_decomposition_gt and _chemical.temperature_decomposition_lt allow a range of temperatures to be given. _chemical.temperature_decomposition should always be used in preference to these two items whenever possible.
Related items: _chemical_temperature_decomposition_gt (cif_core.dic, 2.3)
Type: float
Units: kelvins
Related item: _chemical.temperature_decomposition (alternate)
Range: [0.0, 0.0] [0.0, .]
Example:
350
Category: chemical
Mandatory: no
A temperature in kelvins below which the solid is known to decompose. _chemical.temperature_decomposition_gt and _chemical.temperature_decomposition_lt allow a range of temperatures to be given. _chemical.temperature_decomposition should always be used in preference to these two items whenever possible.
Related items: _chemical_temperature_decomposition_lt (cif_core.dic, 2.3)
Type: float
Units: kelvins
Related item: _chemical.temperature_decomposition (alternate)
Range: [0.0, 0.0] [0.0, .]
Example:
350
Category: chemical
Mandatory: no
The temperature in kelvins at which the solid sublimes.
Related items: _chemical_temperature_sublimation (cif_core.dic, 2.3)
Type: float
Type conditions: esd
Units: kelvins
Related item: _chemical.temperature_sublimation_esd (associated_esd)
Range: [0.0, 0.0] [0.0, .]
Example:
350
Category: chemical
Mandatory: no
The estimated standard deviation of _chemical.temperature_sublimation.
Type: float
Units: kelvins
Related item: _chemical.temperature_sublimation (associated_value)
Category: chemical
Mandatory: no
A temperature in kelvins above which the solid is known to sublime. _chemical.temperature_sublimation_gt and _chemical.temperature_sublimation_lt allow a range of temperatures to be given. _chemical.temperature_sublimation should always be used in preference to these two items whenever possible.
Related items: _chemical_temperature_sublimation_gt (cif_core.dic, 2.3)
Type: float
Units: kelvins
Related item: _chemical.temperature_sublimation (alternate)
Range: [0.0, 0.0] [0.0, .]
Example:
350
Category: chemical
Mandatory: no
A temperature in kelvins below which the solid is known to sublime. _chemical.temperature_sublimation_gt and _chemical.temperature_sublimation_lt allow a range of temperatures to be given. _chemical.temperature_sublimation should always be used in preference to these two items whenever possible.
Related items: _chemical_temperature_sublimation_lt (cif_core.dic, 2.3)
Type: float
Units: kelvins
Related item: _chemical.temperature_sublimation (alternate)
Range: [0.0, 0.0] [0.0, .]
Example:
350
Category: citation
Mandatory: no
Identifier ('refcode') of the database record in the Cambridge Structural Database that contains details of the cited structure.
Related items: _citation_database_id_CSD (cif_core.dic, 2.3)
Type: code
Example:
LEKKUH
Category: database
Mandatory: no
A history of changes made by the Cambridge Crystallographic Data Centre and incorporated into the Cambridge Structural Database (CSD).
Related items: _database_CSD_history (cif_core.dic, 2.3)
Type: text
Category: database
Mandatory: no
The code assigned by Chemical Abstracts.
Related items: _database_code_CAS (cif_core.dic, 2.3)
Type: line
Category: database
Mandatory: no
The code assigned by the Cambridge Structural Database.
Related items: _database_code_CSD (cif_core.dic, 2.3)
Type: line
Category: database
Mandatory: no
The code assigned by the Inorganic Crystal Structure Database.
Related items: _database_code_ICSD (cif_core.dic, 2.3)
Type: line
Category: database
Mandatory: no
The code assigned by the Metals Data File.
Related items: _database_code_MDF (cif_core.dic, 2.3)
Type: line
Category: database
Mandatory: no
The code assigned by the NBS (NIST) Crystal Data Database.
Related items: _database_code_NBS (cif_core.dic, 2.3)
Type: line
Category: database
Mandatory: no
The code assigned by the Protein Data Bank.
Related items: _database_code_PDB (cif_core.dic, 2.3)
Type: line
Category: database
Mandatory: no
The code assigned by the Powder Diffraction File (JCPDS/ICDD).
Related items: _database_code_PDF (cif_core.dic, 2.3)
Type: line
Category: database
Mandatory: no
Deposition numbers assigned by the Fachinformationszentrum Karlsruhe (FIZ) to files containing structural information archived by the Cambridge Crystallographic Data Centre (CCDC).
Related items: _database_code_depnum_ccdc_fiz (cif_core.dic, 2.3)
Type: line
Category: database
Mandatory: no
Deposition numbers assigned by various journals to files containing structural information archived by the Cambridge Crystallographic Data Centre (CCDC).
Related items: _database_code_depnum_ccdc_journal (cif_core.dic, 2.3)
Type: line
Category: database
Mandatory: no
Deposition numbers assigned by the Cambridge Crystallographic Data Centre (CCDC) to files containing structural information archived by the CCDC.
Related items: _database_code_depnum_ccdc_archive (cif_core.dic, 2.3)
Type: line
Category: diffrn
Mandatory: no
The mean hydrostatic pressure in kilopascals at which the intensities were measured.
Related items: _diffrn_ambient_pressure (cif_core.dic, 2.3)
Type: float
Type conditions: esd
Units: kilopascals
Related item: _diffrn.ambient_pressure_esd (associated_esd)
Range: [0.0, 0.0] [0.0, .]
Category: diffrn
Mandatory: no
The estimated standard deviation of _diffrn.ambient_pressure.
Type: float
Units: kilopascals
Related item: _diffrn.ambient_pressure (associated_value)
Category: diffrn
Mandatory: no
The mean hydrostatic pressure in kilopascals above which the intensities were measured. _diffrn.ambient_pressure_gt and _diffrn.ambient_pressure_lt allow a pressure range to be given. _diffrn.ambient_pressure should always be used in preference to these two items whenever possible.
Related items: _diffrn_ambient_pressure_gt (cif_core.dic, 2.3)
Type: float
Units: kilopascals
Related item: _diffrn.ambient_pressure (alternate)
Range: [0.0, 0.0] [0.0, .]
Category: diffrn
Mandatory: no
The mean hydrostatic pressure in kilopascals below which the intensities were measured. _diffrn.ambient_pressure_gt and _diffrn.ambient_pressure_lt allow a pressure range to be given. _diffrn.ambient_pressure should always be used in preference to these two items whenever possible.
Related items: _diffrn_ambient_pressure_lt (cif_core.dic, 2.3)
Type: float
Units: kilopascals
Related item: _diffrn.ambient_pressure (alternate)
Range: [0.0, 0.0] [0.0, .]
Category: diffrn
Mandatory: no
The mean temperature in kelvins above which the intensities were measured. _diffrn.ambient_temp_gt and _diffrn.ambient_temp_lt allow a range of temperatures to be given. _diffrn.ambient_temp should always be used in preference to these two items whenever possible.
Related items: _diffrn_ambient_temperature_gt (cif_core.dic, 2.3)
Type: float
Units: kelvins
Related item: _diffrn.ambient_temp (alternate)
Range: [0.0, 0.0] [0.0, .]
Category: diffrn
Mandatory: no
The mean temperature in kelvins below which the intensities were measured. _diffrn.ambient_temp_gt and _diffrn.ambient_temp_lt allow a range of temperatures to be given. _diffrn.ambient_temp should always be used in preference to these two items whenever possible.
Related items: _diffrn_ambient_temperature_lt (cif_core.dic, 2.3)
Type: float
Units: kelvins
Related item: _diffrn.ambient_temp (alternate)
Range: [0.0, 0.0] [0.0, .]
Category: diffrn_attenuator
Mandatory: no
Material from which the attenuator is made.
Related items: _diffrn_attenuator_material (cif_core.dic, 2.3)
Type: text
Category: diffrn_detector
Mandatory: no
The resolution of an area detector, in pixels/mm.
Related items: _diffrn_detector_area_resol_mean (cif_core.dic, 2.3)
Type: float
Units: pixels_per_millimetre
Range: [0.0, 0.0] [0.0, .]
Category: diffrn_detector
Mandatory: no
The deadtime in microseconds of the detector used to measure the diffraction intensities.
Related items: _diffrn_detector_dtime (cif_core.dic, 2.3)
Type: float
Range: [0.0, 0.0] [0.0, .]
Category: diffrn_refln
Mandatory: no
The code identifying the class to which this reflection has been assigned. This code must match a value of _diffrn_reflns_class.code. Reflections may be grouped into classes for a variety of purposes. For example, for modulated structures each reflection class may be defined by the number m=sum|mi|, where the mi are the integer coefficients that, in addition to h,k,l, index the corresponding diffraction vector in the basis defined for the reciprocal lattice.
Related items: _diffrn_refln_class_code (cif_core.dic, 2.3)
Type: code
Category: diffrn_refln
Mandatory: no
Standard uncertainty of the net intensity calculated from the diffraction counts after the attenuator and standard scales have been applied.
Related items: _diffrn_refln_intensity_u (cif_core.dic, 2.3)
Type: float
Related item: _diffrn_refln.intensity_sigma (alternate)
Range: [0.0, 0.0] [0.0, .]
Category: diffrn_reflns
Mandatory: no
Measure [sum u(net I)|/sum|net I|] for all measured reflections.
Related items: _diffrn_reflns_av_unetI/netI (cif_core.dic, 2.3)
Type: float
Range: [0.0, 0.0] [0.0, .]
Data items in the DIFFRN_REFLNS_CLASS category record details about the classes of reflections measured in the diffraction experiment.
Mandatory: no
Keys: _diffrn_reflns_class.code
Examples:
| Example | Detail |
|---|---|
loop_
_diffrn_reflns_class.number
_diffrn_reflns_class.d_res_high
_diffrn_reflns_class.d_res_low
_diffrn_reflns_class.av_R_eq
_diffrn_reflns_class.code
_diffrn_reflns_class.description
1580 0.551 6.136 0.015 'Main' 'm=0; main reflections'
1045 0.551 6.136 0.010 'Sat1' 'm=1; first-order satellites'
|
Example 1 - example corresponding to the one-dimensional incommensurately modulated structure of K~2~SeO~4~. Each reflection class is defined by the number m=sum|m~i~|, where the m~i~ are the integer coefficients that, in addition to h,k,l, index the corresponding diffraction vector in the basis defined for the reciprocal lattice. |
Category: diffrn_reflns_class
Mandatory: no
For each reflection class, the residual [sum av|del(I)|/sum|av(I)|] for symmetry-equivalent reflections used to calculate the average intensity av(I). The av|del(I)| term is the average absolute difference between av(I) and the individual intensities.
Related items: _diffrn_reflns_class_av_R_eq (cif_core.dic, 2.3)
Type: float
Range: [0.0, 0.0] [0.0, .]
Category: diffrn_reflns_class
Mandatory: no
Measure [sum|sigma(net I)|/sum|net I|] for all measured intensities in a reflection class.
Related items: _diffrn_reflns_class_av_sgI/I (cif_core.dic, 2.3)
Type: float
Related item: _diffrn_reflns_class.av_uI/I (replaces)
Range: [0.0, 0.0] [0.0, .]
Category: diffrn_reflns_class
Mandatory: no
Measure [sum|u(net I)|/sum|net I|] for all measured intensities in a reflection class.
Related items: _diffrn_reflns_class_av_uI/I (cif_core.dic, 2.3)
Type: float
Related item: _diffrn_reflns_class.av_sgI/I (alternate)
Range: [0.0, 0.0] [0.0, .]
Category: diffrn_reflns_class
Mandatory: yes
The code identifying a certain reflection class.
Related items: _diffrn_reflns_class_code (cif_core.dic, 2.3)
Type: code
Examples:
| Example | Detail |
|---|---|
1 |
|
m1 |
|
s2 |
Category: diffrn_reflns_class
Mandatory: no
Description of each reflection class.
Related items: _diffrn_reflns_class_description (cif_core.dic, 2.3)
Type: text
Examples:
| Example | Detail |
|---|---|
m=1 first order satellites |
|
H0L0 common projection reflections |
Category: diffrn_reflns_class
Mandatory: no
The smallest value in angstroms for the interplanar spacings for the reflections in each measured reflection class. This is called the highest resolution for this reflection class.
Related items: _diffrn_reflns_class_d_res_high (cif_core.dic, 2.3)
Type: float
Units: angstroms
Range: [0.0, 0.0] [0.0, .]
Category: diffrn_reflns_class
Mandatory: no
The largest value in angstroms of the interplanar spacings for the reflections for each measured reflection class. This is called the lowest resolution for this reflection class.
Related items: _diffrn_reflns_class_d_res_low (cif_core.dic, 2.3)
Type: float
Units: angstroms
Range: [0.0, 0.0] [0.0, .]
Category: diffrn_reflns_class
Mandatory: no
The total number of measured intensities for each reflection class, excluding the systematic absences arising from centring translations.
Related items: _diffrn_reflns_class_number (cif_core.dic, 2.3)
Type: int
Range: [0, 0] [0, .]
Category: diffrn_source
Mandatory: no
The complement of the angle in degrees between the normal to the surface of the X-ray tube target and the primary X-ray beam for beams generated by traditional X-ray tubes.
Related items: _diffrn_source_take-off_angle (cif_core.dic, 2.3)
Type: float
Units: degrees
Range: [0.00, 0.00] [0.00, 90.0] [90.0, 90.0]
Example:
1.5
Category: diffrn_standards
Mandatory: no
The standard uncertainty of the individual mean standard scales applied to the intensity data.
Related items: _diffrn_standards_scale_u (cif_core.dic, 2.3)
Type: float
Related item: _diffrn_standards.scale_sigma (alternate)
Range: [0.0, 0.0] [0.0, .]
Category: exptl_crystal
Mandatory: no
The enumeration list of standardized names developed for the International Centre for Diffraction Data. The colour of a crystal is given by the combination of _exptl_crystal.colour_modifier with _exptl_crystal.colour_primary, as in 'dark-green' or 'bluish-violet', if necessary combined with _exptl_crystal.colour_lustre, as in 'metallic-green'.
Related items: _exptl_crystal_colour_lustre (cif_core.dic, 2.3)
Type: line
Related item: _exptl_crystal.colour (alternate)
Enumeration values:
| Value | Detail |
|---|---|
metallic |
|
dull |
|
clear |
Category: exptl_crystal
Mandatory: no
The enumeration list of standardized names developed for the International Centre for Diffraction Data. The colour of a crystal is given by the combination of _exptl_crystal.colour_modifier with _exptl_crystal.colour_primary, as in 'dark-green' or 'bluish-violet', if necessary combined with _exptl_crystal.colour_lustre, as in 'metallic-green'.
Related items: _exptl_crystal_colour_modifier (cif_core.dic, 2.3)
Type: line
Related item: _exptl_crystal.colour (alternate)
Enumeration values:
| Value | Detail |
|---|---|
light |
|
dark |
|
whitish |
|
blackish |
|
grayish |
|
brownish |
|
reddish |
|
pinkish |
|
orangish |
|
yellowish |
|
greenish |
|
bluish |
Category: exptl_crystal
Mandatory: no
The enumeration list of standardized names developed for the International Centre for Diffraction Data. The colour of a crystal is given by the combination of _exptl_crystal.colour_modifier with _exptl_crystal.colour_primary, as in 'dark-green' or 'bluish-violet', if necessary combined with _exptl_crystal.colour_lustre, as in 'metallic-green'.
Related items: _exptl_crystal_colour_primary (cif_core.dic, 2.3)
Type: line
Related item: _exptl_crystal.colour (alternate)
Enumeration values:
| Value | Detail |
|---|---|
colourless |
|
white |
|
black |
|
gray |
|
brown |
|
red |
|
pink |
|
orange |
|
yellow |
|
green |
|
blue |
|
violet |
Category: exptl_crystal
Mandatory: no
Density values measured using standard chemical and physical methods. The units are megagrams per cubic metre (grams per cubic centimetre).
Related items: _exptl_crystal_density_meas (cif_core.dic, 2.3)
Type: float
Type conditions: esd
Units: megagrams_per_cubic_metre
Related item: _exptl_crystal.density_meas_esd (associated_esd)
Range: [0.0, 0.0] [0.0, .]
Category: exptl_crystal
Mandatory: no
The estimated standard deviation of _exptl_crystal.density_meas.
Type: float
Units: megagrams_per_cubic_metre
Related item: _exptl_crystal.density_meas (associated_value)
Category: exptl_crystal
Mandatory: no
The value above which the density measured using standard chemical and physical methods lies. The units are megagrams per cubic metre (grams per cubic centimetre). _exptl_crystal.density_meas_gt and _exptl_crystal.density_meas_lt should not be used to report new experimental work, for which _exptl_crystal.density_meas should be used. These items are intended for use in reporting information in existing databases and archives which would be misleading if reported under _exptl_crystal.density_meas.
Related items: _exptl_crystal_density_meas_gt (cif_core.dic, 2.3)
Type: float
Units: megagrams_per_cubic_metre
Related item: _exptl_crystal.density_meas (alternate)
Range: [0.0, 0.0] [0.0, .]
Examples:
| Example | Detail |
|---|---|
2.5 |
lower limit for the density (only the range within which the density lies was given in the original paper) |
Category: exptl_crystal
Mandatory: no
The value below which the density measured using standard chemical and physical methods lies. The units are megagrams per cubic metre (grams per cubic centimetre). _exptl_crystal.density_meas_gt and _exptl_crystal.density_meas_lt should not be used to report new experimental work, for which _exptl_crystal.density_meas should be used. These items are intended for use in reporting information in existing databases and archives which would be misleading if reported under _exptl_crystal.density_meas.
Related items: _exptl_crystal_density_meas_lt (cif_core.dic, 2.3)
Type: float
Units: megagrams_per_cubic_metre
Related item: _exptl_crystal.density_meas (alternate)
Range: [0.0, 0.0] [0.0, .]
Examples:
| Example | Detail |
|---|---|
1.0 |
specimen floats in water |
5.0 |
upper limit for the density (only the range within which the density lies was given in the original paper) |
Category: exptl_crystal
Mandatory: no
Temperature in kelvins at which _exptl_crystal.density_meas was determined.
Related items: _exptl_crystal_density_meas_temp (cif_core.dic, 2.3)
Type: float
Type conditions: esd
Units: kelvins
Range: [0.0, 0.0] [0.0, .]
Category: exptl_crystal
Mandatory: no
The estimated standard deviation of _exptl_crystal.density_meas_temp.
Type: float
Units: kelvins
Category: exptl_crystal
Mandatory: no
Temperature in kelvins above which _exptl_crystal.density_meas was determined. _exptl_crystal.density_meas_temp_gt and _exptl_crystal.density_meas_temp_lt should not be used for reporting new work, for which the correct temperature of measurement should be given. These items are intended for use in reporting information stored in databases or archives which would be misleading if reported under _exptl_crystal.density_meas_temp.
Related items: _exptl_crystal_density_meas_temp_gt (cif_core.dic, 2.3)
Type: float
Units: kelvins
Related item: _exptl_crystal.density_meas_temp (alternate)
Range: [0.0, 0.0] [0.0, .]
Category: exptl_crystal
Mandatory: no
Temperature in kelvins below which _exptl_crystal.density_meas was determined. _exptl_crystal.density_meas_temp_gt and _exptl_crystal.density_meas_temp_lt should not be used for reporting new work, for which the correct temperature of measurement should be given. These items are intended for use in reporting information stored in databases or archives which would be misleading if reported under _exptl_crystal.density_meas_temp.
Related items: _exptl_crystal_density_meas_temp_lt (cif_core.dic, 2.3)
Type: float
Units: kelvins
Related item: _exptl_crystal.density_meas_temp (alternate)
Range: [0.0, 0.0] [0.0, .]
Examples:
| Example | Detail |
|---|---|
300 |
The density was measured at some unspecified temperature below room temperature. |
Category: geom_bond
Mandatory: no
The bond valence calculated from _geom_bond.dist.
Related items: _geom_bond_valence (cif_core.dic, 2.3)
Type: int
Category: publ_author
Mandatory: no
Identifier in the IUCr contact database of a publication author. This identifier may be available from the World Directory of Crystallographers (http://wdc.iucr.org).
Related items: _publ_author_id_iucr (cif_core.dic, 2.3)
Type: code
Example:
2985
Category: refine
Mandatory: no
Residual factor for the reflections (with number given by _reflns.number_gt) judged significantly intense (i.e. satisfying the threshold specified by _reflns.threshold_expression) and included in the refinement. The reflections also satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low. This is the conventional R factor. See also _refine.ls_wR_factor_ definitions. sum | F(obs) - F(calc) | R = ------------------------ sum | F(obs) | F(obs) = the observed structure-factor amplitudes F(calc) = the calculated structure-factor amplitudes and the sum is taken over the specified reflections
Related items: _refine_ls_R_factor_gt (cif_core.dic, 2.3)
Type: float
Related item: _refine.ls_R_factor_obs (alternate)
Range: [0.0, 0.0] [0.0, .]
Category: refine
Mandatory: no
The least-squares goodness-of-fit parameter S for significantly intense reflections (see _reflns.threshold_expression) after the final cycle of refinement. Ideally, account should be taken of parameters restrained in the least-squares refinement. See also _refine.ls_restrained_S_ definitions. { sum { w [ Y(obs) - Y(calc) ]2 } }1/2 S = { ----------------------------------- } { Nref - Nparam } Y(obs) = the observed coefficients (see _refine_ls_structure_factor_coef) Y(calc) = the calculated coefficients (see _refine_ls_structure_factor_coef) w = the least-squares reflection weight [1/(u2)] u = standard uncertainty Nref = the number of reflections used in the refinement Nparam = the number of refined parameters and the sum is taken over the specified reflections
Related items: _refine_ls_goodness_of_fit_gt (cif_core.dic, 2.3)
Type: float
Related item: _refine.ls_goodness_of_fit_obs (alternate)
Range: [0.0, 0.0] [0.0, .]
Category: refine
Mandatory: no
The least-squares goodness-of-fit parameter S for all reflections included in the refinement after the final cycle of refinement. Ideally, account should be taken of parameters restrained in the least-squares refinement. See also _refine_ls_restrained_S_ definitions. { sum | w | Y(obs) - Y(calc) |2 | }1/2 S = { ----------------------------------- } { Nref - Nparam } Y(obs) = the observed coefficients (see _refine_ls_structure_factor_coef) Y(calc) = the calculated coefficients (see _refine_ls_structure_factor_coef) w = the least-squares reflection weight [1/(u2)] u = standard uncertainty Nref = the number of reflections used in the refinement Nparam = the number of refined parameters and the sum is taken over the specified reflections
Related items: _refine_ls_goodness_of_fit_ref (cif_core.dic, 2.3)
Type: float
Range: [0.0, 0.0] [0.0, .]
Category: refine
Mandatory: no
The largest ratio of the final least-squares parameter shift to the final standard uncertainty.
Related items: _refine_ls_shift/su_max (cif_core.dic, 2.3)
Type: float
Related item: _refine.ls_shift_over_esd_max (alternate)
Range: [0.0, 0.0] [0.0, .]
Category: refine
Mandatory: no
An upper limit for the largest ratio of the final least-squares parameter shift to the final standard uncertainty. This item is used when the largest value of the shift divided by the final standard uncertainty is too small to measure.
Related items: _refine_ls_shift/su_max_lt (cif_core.dic, 2.3)
Type: float
Related item: _refine.ls_shift_over_su_max (alternate)
Range: [0.0, 0.0] [0.0, .]
Category: refine
Mandatory: no
The average ratio of the final least-squares parameter shift to the final standard uncertainty.
Related items: _refine_ls_shift/su_mean (cif_core.dic, 2.3)
Type: float
Related item: _refine.ls_shift_over_esd_mean (alternate)
Range: [0.0, 0.0] [0.0, .]
Category: refine
Mandatory: no
An upper limit for the average ratio of the final least-squares parameter shift to the final standard uncertainty. This item is used when the average value of the shift divided by the final standard uncertainty is too small to measure.
Related items: _refine_ls_shift/su_mean_lt (cif_core.dic, 2.3)
Type: float
Related item: _refine.ls_shift_over_su_mean (alternate)
Range: [0.0, 0.0] [0.0, .]
Data items in the REFINE_LS_CLASS category record details about the reflections used for the structure refinement for each reflection class separately.
Mandatory: no
Keys: _refine_ls_class.code
Examples:
| Example | Detail |
|---|---|
loop_
_refine_ls_class.R_factor_gt
_refine_ls_class.code
0.057 'Main'
0.074 'Com'
0.064 'NbRefls'
0.046 'LaRefls'
0.112 'Sat1'
0.177 'Sat2'
|
Example 1 - data for a modulated structure from van Smaalen [J. Phys. Condens. Matter (1991), 3, 1247-1263]. |
Category: refine_ls_class
Mandatory: yes
The code identifying a certain reflection class. This code must match a _reflns_class.code.
Related items: _refine_ls_class_code (cif_core.dic, 2.3)
Type: code
Examples:
| Example | Detail |
|---|---|
1 |
|
m1 |
|
s2 |
Category: refine_ls_class
Mandatory: no
For each reflection class, the lowest value in angstroms for the interplanar spacings for the reflections used in the refinement. This is called the highest resolution.
Related items: _refine_ls_class_d_res_high (cif_core.dic, 2.3)
Type: float
Units: angstroms
Range: [0.0, 0.0] [0.0, .]
Category: refine_ls_class
Mandatory: no
For each reflection class, the highest value in angstroms for the interplanar spacings for the reflections used in the refinement. This is called the lowest resolution.
Related items: _refine_ls_class_d_res_low (cif_core.dic, 2.3)
Type: float
Units: angstroms
Range: [0.0, 0.0] [0.0, .]
Category: refine_ls_class
Mandatory: no
For each reflection class, the residual factor for significantly intense reflections (see _reflns.threshold_expression) included in the refinement. The reflections also satisfy the resolution limits established by _refine_ls_class.d_res_high and _refine_ls_class.d_res_low. This is the conventional R factor. See also the definition of _refine_ls_class.wR_factor_all. sum | F(obs) - F(calc) | R = ------------------------ sum | F(obs) | F(obs) = the observed structure-factor amplitudes F(calc) = the calculated structure-factor amplitudes and the sum is taken over the reflections of this class.
Related items: _refine_ls_class_R_factor_gt (cif_core.dic, 2.3)
Type: float
Range: [0.0, 0.0] [0.0, .]
Category: refine_ls_class
Mandatory: no
For each reflection class, the residual factor for all reflections satisfying the resolution limits established by _refine_ls_class.d_res_high and _refine_ls_class.d_res_low. This is the conventional R factor. See also the definition of _refine_ls_class.wR_factor_all. sum | F(obs) - F(calc) | R = ------------------------ sum | F(obs) | F(obs) = the observed structure-factor amplitudes F(calc) = the calculated structure-factor amplitudes and the sum is taken over the reflections of this class.
Related items: _refine_ls_class_R_factor_all (cif_core.dic, 2.3)
Type: float
Range: [0.0, 0.0] [0.0, .]
Category: refine_ls_class
Mandatory: no
For each reflection class, the residual factor R(F2) calculated on the squared amplitudes of the observed and calculated structure factors, for the reflections judged significantly intense (i.e. satisfying the threshold specified by _reflns.threshold_expression) and included in the refinement. The reflections also satisfy the resolution limits established by _refine_ls_class.d_res_high and _refine_ls_class.d_res_low. sum | F(obs)2 - F(calc)2 | R(Fsqd) = ------------------------------- sum F(obs)2 F(obs)2 = squares of the observed structure-factor amplitudes F(calc)2 = squares of the calculated structure-factor amplitudes and the sum is taken over the reflections of this class.
Related items: _refine_ls_class_R_Fsqd_factor (cif_core.dic, 2.3)
Type: float
Range: [0.0, 0.0] [0.0, .]
Category: refine_ls_class
Mandatory: no
For each reflection class, the residual factor R(I) for the reflections judged significantly intense (i.e. satisfying the threshold specified by _reflns.threshold_expression) and included in the refinement. This is most often calculated in Rietveld refinements against powder data, where it is referred to as RB or RBragg sum | I(obs) - I(calc) | R(I) = ------------------------ sum | I(obs) | I(obs) = the net observed intensities I(calc) = the net calculated intensities and the sum is taken over the reflections of this class.
Related items: _refine_ls_class_R_I_factor (cif_core.dic, 2.3)
Type: float
Range: [0.0, 0.0] [0.0, .]
Category: refine_ls_class
Mandatory: no
For each reflection class, the weighted residual factor for all reflections included in the refinement. The reflections also satisfy the resolution limits established by _refine_ls_class.d_res_high and _refine_ls_class.d_res_low. See also the _refine_ls_class.R_factor_ definitions. ( sum w [ Y(obs) - Y(calc) ]2 )1/2 wR = ( ------------------------------ ) ( sum w Y(obs)2 ) Y(obs) = the observed amplitude specified by _refine.ls_structure_factor_coef Y(calc) = the calculated amplitude specified by _refine.ls_structure_factor_coef w = the least-squares weight and the sum is taken over the reflections of this class.
Related items: _refine_ls_class_wR_factor_all (cif_core.dic, 2.3)
Type: float
Range: [0.0, 0.0] [0.0, .]
Category: refln
Mandatory: no
The code identifying the class to which this reflection has been assigned. This code must match a value of _reflns_class.code. Reflections may be grouped into classes for a variety of purposes. For example, for modulated structures each reflection class may be defined by the number m=sum|mi|, where the mi are the integer coefficients that, in addition to h,k,l, index the corresponding diffraction vector in the basis defined for the reciprocal lattice.
Related items: _refln_class_code (cif_core.dic, 2.3)
Type: code
Category: refln
Mandatory: no
The d spacing in angstroms for this reflection. This is related to the (sin theta)/lambda value by the expression _refln.d_spacing = 2/(_refln.sint/lambda).
Related items: _refln_d_spacing (cif_core.dic, 2.3)
Type: float
Units: angstroms
Range: [0.0, 0.0] [0.0, .]
Category: refln
Mandatory: no
Classification of a reflection so as to indicate its status with respect to inclusion in the refinement and the calculation of R factors.
Related items: _refln_include_status (cif_core.dic, 2.3)
Type: code
Related item: _refln.status (alternate)
Enumeration values:
| Value | Detail |
|---|---|
o |
(lower-case letter o for 'observed') satisfies _refine.ls_d_res_high satisfies _refine.ls_d_res_low exceeds _reflns.threshold_expression |
< |
satisfies _refine.ls_d_res_high satisfies _refine.ls_d_res_low does not exceed _reflns.threshold_expression |
- |
systematically absent reflection |
x |
unreliable measurement -- not used |
h |
does not satisfy _refine.ls_d_res_high |
l |
does not satisfy _refine.ls_d_res_low |
Category: refln
Mandatory: no
Mean path length in millimetres through the crystal for this reflection.
Related items: _refln_mean_path_length_tbar (cif_core.dic, 2.3)
Type: float
Units: millimetres
Range: [0.0, 0.0] [0.0, .]
Category: reflns
Mandatory: no
The proportion of Friedel-related reflections present in the number of 'independent' reflections specified by the item _reflns.number_all. This proportion is calculated as the ratio: [N(Crystal class) - N(Laue symmetry)] / N(Laue symmetry) where, working from the DIFFRN_REFLN list, N(Crystal class) is the number of reflections obtained on averaging under the symmetry of the crystal class N(Laue symmetry) is the number of reflections obtained on averaging under the Laue symmetry. Examples: (a) For centrosymmetric structures, the value of _reflns.Friedel_coverage is necessarily equal to 0.0, as the crystal class is identical to the Laue symmetry. (b) For whole-sphere data for a crystal in the space group P1, _reflns.Friedel_coverage is equal to 1.0, as no reflection h k l is equivalent to -h -k -l in the crystal class and all Friedel pairs {h k l; -h -k -l} have been measured. (c) For whole-sphere data in space group Pmm2, _reflns.Friedel_coverage will be < 1.0 because although reflections h k l and -h -k -l are not equivalent when h k l indices are nonzero, they are when l=0. (d) For a crystal in space group Pmm2, measurements of the two inequivalent octants h >= 0, k >=0, l lead to the same value as in (c), whereas measurements of the two equivalent octants h >= 0, k, l >= 0 will lead to a zero value for _reflns.Friedel_coverage.
Related items: _reflns_Friedel_coverage (cif_core.dic, 2.3)
Type: float
Range: [0.0, 0.0] [0.0, 1.0] [1.0, 1.0]
Category: reflns
Mandatory: no
The number of reflections in the REFLN list (not the DIFFRN_REFLN list) that are significantly intense, satisfying the criterion specified by _reflns.threshold_expression. This may include Friedel-equivalent reflections (i.e. those which are symmetry-equivalent under the Laue symmetry but inequivalent under the crystal class) according to the nature of the structure and the procedures used. Any special characteristics of the reflections included in the REFLN list should be described using the item _reflns.details.
Related items: _reflns_number_gt (cif_core.dic, 2.3)
Type: int
Range: [0, 0] [0, .]
Category: reflns
Mandatory: no
The threshold, usually based on multiples of u(I), u(F2) or u(F), that serves to identify significantly intense reflections, the number of which is given by _reflns.number_gt. These reflections are used in the calculation of _refine.ls_R_factor_gt.
Alias: _reflns_threshold_expression (cif_core.dic, 2.3)
Type: text
Related items: _reflns.observed_criterion (alternate)
Example:
I>2u(I)
Data items in the REFLNS_CLASS category record details of the reflections used to determine the structural parameters for each reflection class.
Mandatory: no
Keys: _reflns_class.code
Examples:
| Example | Detail |
|---|---|
loop_
_reflns_class.number_gt
_reflns_class.code
584 'Main'
226 'Sat1'
50 'Sat2'
|
Example 1 - example corresponding to the one-dimensional incommensurately modulated structure of K~2~SeO~4~. |
Category: reflns_class
Mandatory: yes
The code identifying a certain reflection class.
Related items: _reflns_class_code (cif_core.dic, 2.3)
Type: code
Examples:
| Example | Detail |
|---|---|
1 |
|
m1 |
|
s2 |
Category: reflns_class
Mandatory: no
Description of each reflection class.
Related items: _reflns_class_description (cif_core.dic, 2.3)
Type: text
Examples:
| Example | Detail |
|---|---|
m=1 first order satellites |
|
H0L0 common projection reflections |
Category: reflns_class
Mandatory: no
For each reflection class, the smallest value in angstroms for the interplanar spacings for the reflections used in the refinement. This is called the highest resolution.
Related items: _reflns_class_d_res_high (cif_core.dic, 2.3)
Type: float
Units: angstroms
Range: [0.0, 0.0] [0.0, .]
Category: reflns_class
Mandatory: no
For each reflection class, the largest value in angstroms for the interplanar spacings for the reflections used in the refinement. This is called the lowest resolution.
Related items: _reflns_class_d_res_low (cif_core.dic, 2.3)
Type: float
Units: angstroms
Range: [0.0, 0.0] [0.0, .]
Category: reflns_class
Mandatory: no
For each reflection class, the number of significantly intense reflections (see _reflns.threshold_expression) in the REFLN list (not the DIFFRN_REFLN list). This may include Friedel- equivalent reflections (i.e. those which are symmetry-equivalent under the Laue symmetry but inequivalent under the crystal class) according to the nature of the structure and the procedures used. Any special characteristics of the reflections included in the REFLN list should be described using the item _reflns.details.
Related items: _reflns_class_number_gt (cif_core.dic, 2.3)
Type: int
Range: [0, 0] [0, .]
Category: reflns_class
Mandatory: no
For each reflection class, the total number of reflections in the REFLN list (not the DIFFRN_REFLN list). This may include Friedel-equivalent reflections (i.e. those which are symmetry-equivalent under the Laue symmetry but inequivalent under the crystal class) according to the nature of the structure and the procedures used. Any special characteristics of the reflections included in the REFLN list should be described using the item _reflns.details.
Related items: _reflns_class_number_total (cif_core.dic, 2.3)
Type: int
Range: [0, 0] [0, .]
Category: reflns_class
Mandatory: no
For each reflection class, the residual factor for all reflections included in the refinement. The reflections also satisfy the resolution limits established by _reflns_class.d_res_high and _reflns_class.d_res_low. This is the conventional R factor. See also the definition of _reflns_class.wR_factor_all. sum | F(obs) - F(calc) | R = ------------------------ sum | F(obs) | F(obs) = the observed structure-factor amplitudes F(calc) = the calculated structure-factor amplitudes and the sum is taken over the reflections of this class.
Related items: _reflns_class_R_factor_all (cif_core.dic, 2.3)
Type: float
Range: [0.0, 0.0] [0.0, .]
Category: reflns_class
Mandatory: no
For each reflection class, the residual factor for significantly intense reflections (see _reflns.threshold_expression) included in the refinement. The reflections also satisfy the resolution limits established by _reflns_class.d_res_high and _reflns_class.d_res_low. This is the conventional R factor. See also the definition of _reflns_class.wR_factor_all. sum | F(obs) - F(calc) | R = ------------------------ sum | F(obs) | F(obs) = the observed structure-factor amplitudes F(calc) = the calculated structure-factor amplitudes and the sum is taken over the reflections of this class.
Related items: _reflns_class_R_factor_gt (cif_core.dic, 2.3)
Type: float
Range: [0.0, 0.0] [0.0, .]
Category: reflns_class
Mandatory: no
For each reflection class, the residual factor R(F2) calculated on the squared amplitudes of the observed and calculated structure factors for the reflections judged significantly intense (i.e. satisfying the threshold specified by _reflns.threshold_expression) and included in the refinement. The reflections also satisfy the resolution limits established by _reflns_class.d_res_high and _reflns_class.d_res_low. sum | F(obs)2 - F(calc)2 | R(Fsqd) = ------------------------------- sum F(obs)2 F(obs)2 = squares of the observed structure-factor amplitudes F(calc)2 = squares of the calculated structure-factor amplitudes and the sum is taken over the reflections of this class.
Related items: _reflns_class_R_Fsqd_factor (cif_core.dic, 2.3)
Type: float
Range: [0.0, 0.0] [0.0, .]
Category: reflns_class
Mandatory: no
For each reflection class, the residual factor R(I) for the reflections judged significantly intense (i.e. satisfying the threshold specified by _reflns.threshold_expression) and included in the refinement. This is most often calculated in Rietveld refinements against powder data, where it is referred to as RB or RBragg. sum | I(obs) - I(calc) | R(I) = ------------------------ sum | I(obs) | I(obs) = the net observed intensities I(calc) = the net calculated intensities and the sum is taken over the reflections of this class.
Related items: _reflns_class_R_I_factor (cif_core.dic, 2.3)
Type: float
Range: [0.0, 0.0] [0.0, .]
Category: reflns_class
Mandatory: no
For each reflection class, the weighted residual factors for all reflections included in the refinement. The reflections also satisfy the resolution limits established by _reflns_class.d_res_high and _reflns_class.d_res_low. See also _reflns_class.R_factor_ definitions. ( sum w [ Y(obs) - Y(calc) ]2 )1/2 wR = ( ------------------------------ ) ( sum w Y(obs)2 ) Y(obs) = the observed amplitude specified by _refine.ls_structure_factor_coef Y(calc) = the calculated amplitude specified by _refine.ls_structure_factor_coef w = the least-squares weight and the sum is taken over the reflections of this class.
Related items: _reflns_class_wR_factor_all (cif_core.dic, 2.3)
Type: float
Range: [0.0, 0.0] [0.0, .]
Category: reflns_shell
Mandatory: no
The ratio of the mean of the intensities of the significantly intense reflections (see _reflns.threshold_expression) in this shell to the mean of the standard uncertainties of the intensities of the significantly intense reflections in this shell.
Related items: _reflns_shell_meanI_over_sigI_gt (cif_core.dic, 2.3)
Type: float
Related item: _reflns_shell.meanI_over_uI_gt (replaces)
Category: reflns_shell
Mandatory: no
The ratio of the mean of the intensities of all reflections in this shell to the mean of the standard uncertainties of the intensities of all reflections in this shell.
Related items: _reflns_shell_meanI_over_uI_all (cif_core.dic, 2.3)
Type: float
Related item: _reflns_shell.meanI_over_sigI_all (alternate)
Category: reflns_shell
Mandatory: no
The ratio of the mean of the intensities of the significantly intense reflections (see _reflns.threshold_expression) in this shell to the mean of the standard uncertainties of the intensities of the significantly intense reflections in this shell.
Related items: _reflns_shell_meanI_over_uI_gt (cif_core.dic, 2.3)
Type: float
Related items: _reflns_shell.meanI_over_sigI_gt (alternate) _reflns_shell.meanI_over_sigI_obs (alternate)
Category: reflns_shell
Mandatory: no
The number of significantly intense reflections (see _reflns.threshold_expression) measured for this shell.
Related items: _reflns_shell_number_measured_gt (cif_core.dic, 2.3)
Type: int
Related item: _reflns_shell.number_measured_obs (alternate)
Range: [0, 0] [0, .]
Category: reflns_shell
Mandatory: no
The total number of significantly intense reflections (see _reflns.threshold_expression) resulting from merging measured symmetry-equivalent reflections for this resolution shell.
Related items: _reflns_shell_number_unique_gt (cif_core.dic, 2.3)
Type: int
Related item: _reflns_shell.number_unique_obs (alternate)
Range: [0, 0] [0, .]
Category: reflns_shell
Mandatory: no
The percentage of geometrically possible reflections represented by significantly intense reflections (see _reflns.threshold_expression) measured for this shell.
Related items: _reflns_shell_percent_possible_gt (cif_core.dic, 2.3)
Type: float
Related item: _reflns_shell.percent_possible_obs (alternate)
Range: [0.0, 0.0] [0.0, 100.0] [100.0, 100.0]
Category: reflns_shell
Mandatory: no
The value of Rmerge(F) for significantly intense reflections (see _reflns.threshold_expression) in a given shell. sumi ( sumj | Fj - <F> | ) Rmerge(F) = -------------------------------- sumi ( sumj <F> ) Fj = the amplitude of the jth observation of reflection i <F> = the mean of the amplitudes of all observations of reflection i sumi is taken over all reflections sumj is taken over all observations of each reflection.
Related items: _reflns_shell_Rmerge_F_gt (cif_core.dic, 2.3)
Type: float
Related item: _reflns_shell.Rmerge_F_obs (alternate)
Range: [0.0, 0.0] [0.0, .]
Category: reflns_shell
Mandatory: no
The value of Rmerge(I) for significantly intense reflections (see _reflns.threshold_expression) in a given shell. sumi ( sumj | Ij - <I> | ) Rmerge(I) = -------------------------------- sumi ( sumj <I> ) Ij = the intensity of the jth observation of reflection i <I> = the mean of the intensities of all observations of reflection i sumi is taken over all reflections sumj is taken over all observations of each reflection.
Related items: _reflns_shell_Rmerge_I_gt (cif_core.dic, 2.3)
Type: float
Related item: _reflns_shell.Rmerge_I_obs (alternate)
Range: [0.0, 0.0] [0.0, .]
Contains all the data items that refer to the space group as a whole, such as its name or crystal system. They may be looped, for example, in a list of space groups and their properties. Only a subset of the SPACE_GROUP category items appear in this dictionary. The remainder are found in the symmetry CIF dictionary. Space-group types are identified by their number as given in International Tables for Crystallography Vol. A. Specific settings of the space groups can be identified either by their Hall symbol or by specifying their symmetry operations. The commonly used Hermann-Mauguin symbol determines the space-group type uniquely but several different Hermann-Mauguin symbols may refer to the same space-group type. A Hermann-Mauguin symbol contains information on the choice of the basis, but not on the choice of origin. Different formats for the Hermann-Mauguin symbol are found in the symmetry CIF dictionary.
Mandatory: no
Keys: _space_group.id
Examples:
| Example | Detail |
|---|---|
_space_group.id 1
_space_group.name_H-M_alt 'C 2/c'
_space_group.IT_number 15
_space_group.name_Hall '-C 2yc'
_space_group.crystal_system monoclinic
|
Example 1 - the monoclinic space group No. 15 with unique axis b. |
Category: space_group
Mandatory: no
The name of the system of geometric crystal classes of space groups (crystal system) to which the space group belongs. Note that rhombohedral space groups belong to the trigonal system.
Related items: _space_group_crystal_system (cif_core.dic, 2.3)
Type: code
Related item: _symmetry.cell_setting (alternate)
Enumeration values:
| Value | Detail |
|---|---|
triclinic |
|
monoclinic |
|
orthorhombic |
|
tetragonal |
|
trigonal |
|
hexagonal |
|
cubic |
Category: space_group
Mandatory: yes
This is the unique identifier for the SPACE_GROUP category.
Related items: _space_group_id (cif_core.dic, 2.3)
Type: code
Category: space_group
Mandatory: no
The number as assigned in International Tables for Crystallography Vol. A, specifying the proper affine class (i.e. the orientation-preserving affine class) of space groups (crystallographic space-group type) to which the space group belongs. This number defines the space-group type but not the coordinate system in which it is expressed.
Related items: _space_group_IT_number (cif_core.dic, 2.3)
Type: int
Related item: _symmetry.Int_Tables_number (alternate)
Range: [1, 1] [1, 230] [230, 230]
Category: space_group
Mandatory: no
Space-group symbol defined by Hall. Each component of the space-group name is separated by a space or an underscore. The use of a space is strongly recommended. The underscore is only retained because it was used in old CIFs. It should not be used in new CIFs. _space_group.name_Hall uniquely defines the space group and its reference to a particular coordinate system. Ref: Hall, S. R. (1981). Acta Cryst. A37, 517-525; erratum (1981), A37, 921. [See also International Tables for Crystallography Vol. B (2001), Chapter 1.4, Appendix 1.4.2.]
Related items: _space_group_name_Hall (cif_core.dic, 2.3)
Type: line
Related item: _symmetry.space_group_name_Hall (alternate)
Examples:
| Example | Detail |
|---|---|
P 2c -2ac |
equivalent to Pca21 |
-I 4bd 2ab 3 |
equivalent to Ia3d |
Category: space_group
Mandatory: no
_space_group.name_H-M_alt allows any Hermann-Mauguin symbol to be given. The way in which this item is used is determined by the user and in general is not intended to be interpreted by computer. It may, for example, be used to give one of the extended Hermann-Mauguin symbols given in Table 4.3.2.1 of International Tables for Crystallography Vol. A (2002) or a Hermann-Mauguin symbol for a conventional or unconventional setting. Each component of the space-group name is separated by a space or an underscore. The use of a space is strongly recommended. The underscore is only retained because it was used in old CIFs. It should not be used in new CIFs. Subscripts should appear without special symbols. Bars should be given as negative signs before the numbers to which they apply. The commonly used Hermann-Mauguin symbol determines the space- group type uniquely but a given space-group type may be described by more than one Hermann-Mauguin symbol. The space- group type is best described using _space_group.IT_number. The Hermann-Mauguin symbol may contain information on the choice of basis, but not on the choice of origin. To define the setting uniquely, use _space_group.name_Hall or list the symmetry operations.
Related items: _space_group_name_H-M_alt (cif_core.dic, 2.3)
Type: line
Related item: _symmetry.space_group_name_H-M (alternate)
Examples:
| Example | Detail |
|---|---|
loop_
_space_group.name_H-M_alt
'C m c m'
'C 2/c 2/m 21/m'
'A m a m'
|
three examples for space group No. 63 |
Contains information about the symmetry operations of the space group.
Mandatory: no
Keys: _space_group_symop.id
Examples:
| Example | Detail |
|---|---|
loop_
_space_group_symop.id
_space_group_symop.operation_xyz
1 x,y,z
2 -x,-y,-z
3 -x,1/2+y,1/2-z
4 x,1/2-y,1/2+z
|
Example 1 - The symmetry operations for the space group P21/c. |
Category: space_group_symop
Mandatory: yes
An arbitrary identifier that uniquely labels each symmetry operation in the list.
Related items: _space_group_symop_id (cif_core.dic, 2.3)
Type: code
Related item: _symmetry_equiv.id (alternate)
Category: space_group_symop
Mandatory: no
A parsable string giving one of the symmetry operations of the space group in algebraic form. If W is a matrix representation of the rotational part of the symmetry operation defined by the positions and signs of x, y and z, and w is a column of translations defined by the fractions, an equivalent position X' is generated from a given position X by the equation X' = WX + w (Note: X is used to represent bold_italics_x in International Tables for Crystallography Vol. A, Part 5) When a list of symmetry operations is given, it must contain a complete set of coordinate representatives which generates all the operations of the space group by the addition of all primitive translations of the space group. Such representatives are to be found as the coordinates of the general-equivalent position in International Tables for Crystallography Vol. A (2002), to which it is necessary to add any centring translations shown above the general-equivalent position. That is to say, it is necessary to list explicity all the symmetry operations required to generate all the atoms in the unit cell defined by the setting used.
Related items: _space_group_symop_operation_xyz (cif_core.dic, 2.3)
Type: line
Related item: _symmetry_equiv.pos_as_xyz (alternate)
Examples:
| Example | Detail |
|---|---|
x,1/2-y,1/2+z |
glide reflection through the plane (x,1/4,z), with glide vector 1/2 c |
Category: space_group_symop
Mandatory: no
This must match a particular value of _space_group.id, allowing the symmetry operation to be identified with a particular space group.
Related items: _space_group_symop_sg_id (cif_core.dic, 2.3)
Type: code
Data items in the VALENCE_PARAM category define the parameters used for calculating bond valences from bond lengths. In addition to the parameters, a pointer is given to the reference (in VALENCE_REF) from which the bond-valence parameters were taken.
Mandatory: no
Keys: _valence_param.atom_1 _valence_param.atom_1_valence _valence_param.atom_2 _valence_param.atom_2_valence
Examples:
| Example | Detail |
|---|---|
loop_
_valence_param.atom_1
_valence_param.atom_1_valence
_valence_param.atom_2
_valence_param.atom_2_valence
_valence_param.Ro
_valence_param.B
_valence_param.ref_id
_valence_param.details
Cu 2 O -2 1.679 0.37 a .
Cu 2 O -2 1.649 0.37 j .
Cu 2 N -3 1.64 0.37 m '2-coordinate N'
Cu 2 N -3 1.76 0.37 m '3-coordinate N'
loop_
_valence_ref.id
_valence_ref.reference
a 'Brown & Altermatt (1985), Acta Cryst. B41, 244-247'
j 'Liu & Thorp (1993), Inorg. Chem. 32, 4102-4205'
m 'See, Krause & Strub (1998), Inorg. Chem. 37, 5369-5375'
|
Example 1 - a bond-valence parameter list with accompanying references. |
Category: valence_param
Mandatory: yes
The element symbol of the first atom forming the bond whose bond-valence parameters are given in this category.
Related items: _valence_param_atom_1 (cif_core.dic, 2.3)
Type: code
Category: valence_param
Mandatory: yes
The valence (formal charge) of the first atom whose bond-valence parameters are given in this category.
Related items: _valence_param_atom_1_valence (cif_core.dic, 2.3)
Type: int
Category: valence_param
Mandatory: yes
The element symbol of the second atom forming the bond whose bond-valence parameters are given in this category.
Related items: _valence_param_atom_2 (cif_core.dic, 2.3)
Type: code
Category: valence_param
Mandatory: yes
The valence (formal charge) of the second atom whose bond-valence parameters are given in this category.
Related items: _valence_param_atom_2_valence (cif_core.dic, 2.3)
Type: int
Category: valence_param
Mandatory: no
The bond-valence parameter B used in the expression s = exp[(Ro - R)/B] where s is the valence of a bond of length R.
Related items: _valence_param_B (cif_core.dic, 2.3)
Type: float
Units: angstroms
Category: valence_param
Mandatory: no
Details of or comments on the bond-valence parameters.
Related items: _valence_param_details (cif_core.dic, 2.3)
Type: text
Category: valence_param
Mandatory: no
An identifier for the valence parameters of a bond between the given atoms.
Related items: _valence_param_id (cif_core.dic, 2.3)
Type: code
Category: valence_param
Mandatory: no
An identifier which links to the reference to the source from which the bond-valence parameters are taken. A child of _valence_ref.id which it must match.
Related items: _valence_param_ref_id (cif_core.dic, 2.3)
Type: code
Category: valence_param
Mandatory: no
The bond-valence parameter Ro used in the expression s = exp[(Ro - R)/B] where s is the valence of a bond of length R.
Related items: _valence_param_Ro (cif_core.dic, 2.3)
Type: float
Units: angstroms
Data items in the VALENCE_REF category list the references from which the bond-valence parameters have been taken.
Mandatory: no
Keys: _valence_ref.id
Category: valence_ref
Mandatory: yes
An identifier for items in this category. Parent of _valence_param.ref_id, which must have the same value.
Related items: _valence_ref_id (cif_core.dic, 2.3)
Type: code
Category: valence_ref
Mandatory: no
Literature reference from which the valence parameters identified by _valence_param.id were taken.
Related items: _valence_ref_reference (cif_core.dic, 2.3)
Type: text