Data items in the ATOM_SITE category record details about the atom sites in a crystal structure, such as the positional coordinates, atomic displacement parameters, and magnetic moments and directions.

Category: category_overview

Type: null

Examples:

    loop_
    _atom_site_label
    _atom_site_fract_x
    _atom_site_fract_y
    _atom_site_fract_z
    _atom_site_U_iso_or_equiv
    _atom_site_adp_type
    _atom_site_calc_flag
    _atom_site_calc_attached_atom
      O1   .4154(4)  .5699(1)  .3026(0)  .060(1)  Uani  ?    ?
      C2   .5630(5)  .5087(2)  .3246(1)  .060(2)  Uani  ?    ?
      C3   .5350(5)  .4920(2)  .3997(1)  .048(1)  Uani  ?    ?
      N4   .3570(3)  .5558(1)  .4167(0)  .039(1)  Uani  ?    ?
      C5   .3000(5)  .6122(2)  .3581(1)  .045(1)  Uani  ?    ?
      O21  .6958(5)  .4738(2)  .2874(1)  .090(2)  Uani  ?    ?
      C31  .4869(6)  .3929(2)  .4143(2)  .059(2)  Uani  ?    ?
     # - - - - data truncated for brevity - - - -
      H321C  .04(1)  .318(3)   .320(2)   .14000   Uiso  ?    ?
      H322A  .25(1)  .272(4)   .475(3)   .19000   Uiso  ?    ?
      H322B  .34976  .22118    .40954    .19000   Uiso  calc C322
      H322C  .08(1)  .234(4)   .397(3)   .19000   Uiso  ?    ?

    loop_
    _atom_site_aniso_label
    _atom_site_aniso_B_11
    _atom_site_aniso_B_22
    _atom_site_aniso_B_33
    _atom_site_aniso_B_12
    _atom_site_aniso_B_13
    _atom_site_aniso_B_23
    _atom_site_aniso_type_symbol
     O1   .071(1) .076(1) .0342(9) .008(1)   .0051(9) -.0030(9) O
     C2   .060(2) .072(2) .047(1)  .002(2)   .013(1)  -.009(1)  C
     C3   .038(1) .060(2) .044(1)  .007(1)   .001(1)  -.005(1)  C
     N4   .037(1) .048(1) .0325(9) .0025(9)  .0011(9) -.0011(9) N
     C5   .043(1) .060(1) .032(1)  .001(1)  -.001(1)   .001(1)  C
     # - - - - data truncated for brevity - - - -
     O21  .094(2) .109(2) .068(1)  .023(2)   .038(1)  -.010(1)  O
     C51  .048(2) .059(2) .049(1)  .002(1)  -.000(1)   .007(1)  C
     C511 .048(2) .071(2) .097(3) -.008(2)  -.003(2)   .010(2)  C
     C512 .078(2) .083(2) .075(2)  .009(2)  -.005(2)   .033(2)  C
     C513 .074(2) .055(2) .075(2)  .004(2)   .001(2)  -.010(2)  C
     # - - - - data truncated for brevity - - - -

    loop_
    _atom_site_label
    _atom_site_chemical_conn_number
    _atom_site_fract_x
    _atom_site_fract_y
    _atom_site_fract_z
    _atom_site_U_iso_or_equiv
     S1  1  0.74799(9)  -0.12482(11)  0.27574(9)  0.0742(3)
     S2  2  1.08535(10)  0.16131(9)   0.34061(9)  0.0741(3)
     N1  3  1.0650(2)   -0.1390(2)    0.2918(2)   0.0500(5)
     C1  4  0.9619(3)   -0.0522(3)    0.3009(2)   0.0509(6)
     # - - - - data truncated for brevity - - - -

     loop_
      _atom_site_label                  # *_assembly 'M' is a disordered methyl
      _atom_site_occupancy              # with configurations 'A' and 'B':
      _atom_site_disorder_assembly      #
      _atom_site_disorder_group         #    H11B    H11A      H13B
                                        #      .      |      .
   C1     1      .       .              #        .    |    .
   H11A   .5     M       A              #          .  |  .
   H12A   .5     M       A              #             C1 --------C2---
   H13A   .5     M       A              #           / .  \
   H11B   .5     M       B              #         /   .    \
   H12B   .5     M       B              #       /     .      \
   H13B   .5     M       B              #    H12A    H12B    H13A

A standard code used to describe the type of atomic displacement parameters used for the site.

Category: atom_site

Type: char

List: yes

List reference: _atom_site_label

Related item: _atom_site_thermal_displace_type (alternate)

Enumeration values:

Uani

Uiso

Uovl

Umpe

Bani

Biso

Bovl

These are the standard anisotropic atomic displacement components in angstroms squared which appear in the structure-factor term T = exp{-(1/4) sum_i [ sum_j (B^ij h_i h_j a*_i a*_j) ] } h = the Miller indices a* = the reciprocal-space cell lengths 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.

Category: atom_site

Type: numb

Type conditions: esd

Units: A^2^

Units detail: angstroms squared

List: yes

List reference: _atom_site_aniso_label

Related item: _atom_site_aniso_U_ (conversion)

Anisotropic atomic displacement parameters are usually looped in a separate list. If this is the case, this code must match the _atom_site_label of the associated atom in the atom coordinate list and conform with the same rules described in _atom_site_label.

Category: atom_site

Type: char

List: yes

Link parent: _atom_site_label

Ratio of the maximum to minimum principal axes of displacement (thermal) ellipsoids.

Category: atom_site

Type: numb

List: yes

List reference: _atom_site_aniso_label

Range: [1.0:]

This _atom_type_symbol code links the anisotropic atom parameters to the atom-type data associated with this site and must match one of the _atom_type_symbol codes in this list.

Category: atom_site

Type: char

List: yes

List reference: _atom_site_aniso_label

Link parent: _atom_site_type_symbol

These are the standard anisotropic atomic displacement components in angstroms squared which appear in the structure-factor term T = exp{-2pi² sum_i [sum_j (U^ij h_i h_j a*_i a*_j) ] } h = the Miller indices a* = the reciprocal-space cell lengths The unique elements of the real symmetric matrix are entered by row.

Category: atom_site

Type: numb

Type conditions: esd

Units: A^2^

Units detail: angstroms squared

List: yes

List reference: _atom_site_aniso_label

Related item: _atom_site_aniso_B_ (conversion)

The number of hydrogen atoms attached to the atom at this site excluding any hydrogen atoms for which coordinates (measured or calculated) are given.

Category: atom_site

Type: numb

List: yes

List reference: _atom_site_label

Default value: 0

Range: [0:8]

Examples:

2

1

4

Equivalent isotropic atomic displacement parameter, B(equiv), in angstroms squared, calculated as the geometric mean of the anisotropic atomic displacement parameters. B(equiv) = (B_i B_j B_k)^1/3 B_n = the principal components of the orthogonalized B^ij The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred.

Category: atom_site

Type: numb

Type conditions: esd

Units: A^2^

Units detail: angstroms squared

List: yes

List reference: _atom_site_label

Related items: _atom_site_B_iso_or_equiv (alternate) _atom_site_U_equiv_geom_mean (conversion)

Range: [0.0:]

Isotropic atomic displacement parameter, or equivalent isotropic atomic displacement parameter, B(equiv), in angstroms squared, calculated from anisotropic displacement components. B(equiv) = (1/3) sum_i[sum_j(B^ij a*_i a*_j a_i a_j)] a = the real-space cell lengths a* = the reciprocal-space cell lengths B^ij = 8 pi² U^ij 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.

Category: atom_site

Type: numb

Type conditions: esd

Units: A^2^

Units detail: angstroms squared

List: yes

List reference: _atom_site_label

Related items: _atom_site_B_equiv_geom_mean (alternate) _atom_site_U_iso_or_equiv (conversion)

Range: [0.0:]

The _atom_site_label of the atom site to which the 'geometry- calculated' atom site is attached.

Category: atom_site

Type: char

List: yes

List reference: _atom_site_label

Default value: .

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 coordinates. The abbreviation 'c' may be used in place of 'calc'.

Category: atom_site

Type: char

List: yes

List reference: _atom_site_label

Default value: d

Enumeration values:

d

calc

c

dum

The atom-site coordinates in angstroms specified according to a set of orthogonal Cartesian axes related to the cell axes as specified by the _atom_sites_Cartn_transform_axes description.

Category: atom_site

Type: numb

Type conditions: esd

Units: A

Units detail: angstroms

List: yes

List reference: _atom_site_label

Related item: _atom_site_fract_ (alternate)

This number links an atom site to the chemical connectivity list. It must match a number specified by _chemical_conn_atom_number.

Category: atom_site

Type: numb

List: yes

List reference: _atom_site_label

Link parent: _chemical_conn_atom_number

Range: [1:]

A description of the constraints applied to parameters at this site during refinement. See also _atom_site_refinement_flags and _refine_ls_number_constraints.

Category: atom_site

Type: char

List: yes

List reference: _atom_site_label

Default value: .

Example:

pop=1.0-pop(Zn3)

A description of special aspects of this site. See also _atom_site_refinement_flags.

Category: atom_site

Type: char

List: yes

List reference: _atom_site_label

Example:

Ag/Si disordered

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.

Category: atom_site

Type: char

List: yes

List reference: _atom_site_label

Examples:

A

B

S

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.

Category: atom_site

Type: char

List: yes

List reference: _atom_site_label

Examples:

1

2

-1

Atom-site coordinates as fractions of the _cell_length_ values.

Category: atom_site

Type: numb

Type conditions: esd

List: yes

List reference: _atom_site_label

Related item: _atom_site_Cartn_ (alternate)

The _atom_site_label is a unique identifier for a particular site in the crystal. This code is made up of a sequence of up to seven components, _atom_site_label_component_0 to *_6, which may be specified as separate data items. Component 0 usually matches one of the specified _atom_type_symbol codes. This is not mandatory if an _atom_site_type_symbol item is included in the atom-site list. The _atom_site_type_symbol always takes precedence over an _atom_site_label in the identification of the atom type. The label components 1 to 6 are optional, and normally only components 0 and 1 are used. Note that components 0 and 1 are concatenated, while all other components, if specified, are separated by an underscore. Underscores are only used if higher-order components exist. If an intermediate component is not used, it may be omitted provided the underscore separators are inserted. For example, the label 'C233__ggg' is acceptable and represents the components C, 233, '' and ggg. Different labels may have a different number of components.

Category: atom_site

Type: char

List: yes

List mandatory: yes

Link children: _atom_site_aniso_label _geom_angle_atom_site_label_1 _geom_angle_atom_site_label_2 _geom_angle_atom_site_label_3 _geom_bond_atom_site_label_1 _geom_bond_atom_site_label_2 _geom_contact_atom_site_label_1 _geom_contact_atom_site_label_2 _geom_hbond_atom_site_label_D _geom_hbond_atom_site_label_H _geom_hbond_atom_site_label_A _geom_torsion_atom_site_label_1 _geom_torsion_atom_site_label_2 _geom_torsion_atom_site_label_3 _geom_torsion_atom_site_label_4

Examples:

C12

Ca3g28

Fe3+17

H*251

boron2a

C_a_phe_83_a_0

Zn_Zn_301_A_0

Component 0 is normally a code which matches identically with one of the _atom_type_symbol codes. If this is the case, then the rules governing the _atom_type_symbol code apply. If, however, the data item _atom_site_type_symbol is also specified in the atom-site list, component 0 need not match this symbol or adhere to any of the _atom_type_symbol rules. Component 1 is referred to as the "atom number". When component 0 is the atom-type code, it is used to number the sites with the same atom type. This component code must start with at least one digit which is not followed by a + or - sign (to distinguish it from the component 0 rules). Components 2 to 6 contain the identifier, residue, sequence, asymmetry identifier and alternate codes, respectively. These codes may be composed of any characters except an underscore.

Category: atom_site

Type: char

List: yes

List reference: _atom_site_label

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. The value must lie in the 99.97% Gaussian confidence interval -3u =< x =< 1 + 3u. The _enumeration_range of 0.0:1.0 is thus correctly interpreted as meaning (0.0 - 3u) =< x =< (1.0 + 3u).

Category: atom_site

Type: numb

Type conditions: esd

List: yes

List reference: _atom_site_label

Default value: 1.0

Range: [0.0:1.0]

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 legacy CIFs.

Category: atom_site

Type: char

List: yes

List reference: _atom_site_label

Related items: _atom_site_refinement_flags_posn (replace) _atom_site_refinement_flags_adp (replace) _atom_site_refinement_flags_occupancy (replace)

Enumeration values:

.

S

G

R

D

T

U

P

A code which indicates the refinement restraints or constraints applied to the atomic displacement parameters of this site.

Category: atom_site

Type: char

List: yes

List reference: _atom_site_label

Related item: _atom_site_refinement_flags (alternate)

Enumeration values:

.

T

U

TU

A code which indicates that refinement restraints or constraints were applied to the occupancy of this site.

Category: atom_site

Type: char

List: yes

List reference: _atom_site_label

Related item: _atom_site_refinement_flags (alternate)

Enumeration values:

.

P

A code which indicates the refinement restraints or constraints applied to the positional coordinates of this site.

Category: atom_site

Type: char

List: yes

List reference: _atom_site_label

Related item: _atom_site_refinement_flags (alternate)

Enumeration values:

.

D

G

R

S

DG

DR

DS

GR

GS

RS

DGR

DGS

DRS

GRS

DGRS

A description of restraints applied to specific parameters at this site during refinement. See also _atom_site_refinement_flags and _refine_ls_number_restraints.

Category: atom_site

Type: char

List: yes

List reference: _atom_site_label

Example:

restrained to planar ring

The multiplicity of a site due to the space-group symmetry as given in International Tables for Crystallography Vol. A (2002).

Category: atom_site

Type: numb

List: yes

List reference: _atom_site_label

Range: [1:192]

A standard code used to describe the type of atomic displacement parameters used for the site.

Category: atom_site

Type: char

List: yes

List reference: _atom_site_label

Related item: _atom_site_adp_type (replace)

Enumeration values:

Uani

Uiso

Uovl

Umpe

Bani

Biso

Bovl

A code to identify the atom species (singular or plural) occupying this site. This code must match a corresponding _atom_type_symbol. The specification of this code is optional if component 0 of the _atom_site_label is used for this purpose. See _atom_type_symbol.

Category: atom_site

Type: char

List: yes

List reference: _atom_site_label

Link parent: _atom_type_symbol

Link child: _atom_site_aniso_type_symbol

Examples:

Cu

Cu2+

dummy

Fe3+Ni2+

S-

H*

H(SDS)

Equivalent isotropic atomic displacement parameter, U(equiv), in angstroms squared, calculated as the geometric mean of the anisotropic atomic displacement parameters. U(equiv) = (U_i U_j U_k)^1/3 U_n = the principal components of the orthogonalized U^ij

Category: atom_site

Type: numb

Type conditions: esd

Units: A^2^

Units detail: angstroms squared

List: yes

List reference: _atom_site_label

Related items: _atom_site_U_iso_or_equiv (alternate) _atom_site_B_equiv_geom_mean (conversion)

Range: [0.0:]

Isotropic atomic displacement parameter, or equivalent isotropic atomic displacement parameter, U(equiv), in angstroms squared, calculated from anisotropic atomic displacement parameters. U(equiv) = (1/3) sum_i[sum_j(U^ij a*_i a*_j 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.

Category: atom_site

Type: numb

Type conditions: esd

Units: A^2^

Units detail: angstroms squared

List: yes

List reference: _atom_site_label

Related items: _atom_site_U_equiv_geom_mean (alternate) _atom_site_B_iso_or_equiv (conversion)

Range: [0.0:]

The Wyckoff symbol (letter) as listed in the space-group tables of International Tables for Crystallography Vol. A (2002).

Category: atom_site

Type: char

List: yes

List reference: _atom_site_label

Data items in the ATOM_SITES category record details about the crystallographic cell and cell transformations, which are common to all atom sites.

Category: category_overview

Type: null

Examples:

    _atom_sites_Cartn_transform_axes
          'c along z, astar along x, b along y'

    _atom_sites_Cartn_tran_matrix_11    58.39
    _atom_sites_Cartn_tran_matrix_12     0.00
    _atom_sites_Cartn_tran_matrix_13     0.00
    _atom_sites_Cartn_tran_matrix_21     0.00
    _atom_sites_Cartn_tran_matrix_22    86.70
    _atom_sites_Cartn_tran_matrix_23     0.00
    _atom_sites_Cartn_tran_matrix_31     0.00
    _atom_sites_Cartn_tran_matrix_32     0.00
    _atom_sites_Cartn_tran_matrix_33    46.27

Matrix elements used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates. The axial alignments of this transformation are described in _atom_sites_Cartn_transform_axes. The 3 x 1 translation is defined in _atom_sites_Cartn_tran_vector_. x' |11 12 13| x | 1 | ( y' ) Cartesian = |21 22 23| ( y ) fractional + | 2 | z' |31 32 33| z | 3 |

Category: atom_sites

Type: numb

Elements of a 3 x 1 translation vector used in the transformation of fractional coordinates in the ATOM_SITE category to Cartesian coordinates. The axial alignments of this transformation are described in _atom_sites_Cartn_transform_axes. x' |11 12 13| x | 1 | ( y' ) Cartesian = |21 22 23| ( y ) fractional + | 2 | z' |31 32 33| z | 3 |

Category: atom_sites

Type: numb

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_tran_matrix_.

Category: atom_sites

Type: char

Example:

a parallel to x; b in the plane of y and z

Matrix elements used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates. The axial alignments of this transformation are described in _atom_sites_Cartn_transform_axes. The 3 x 1 translation is defined in _atom_sites_fract_tran_vector_. x' |11 12 13| x | 1 | ( y' ) fractional = |21 22 23| ( y ) Cartesian + | 2 | z' |31 32 33| z | 3 |

Category: atom_sites

Type: numb

Elements of a 3 x 1 translation vector used in the transformation of Cartesian coordinates in the ATOM_SITE category to fractional coordinates. The axial alignments of this transformation are described in _atom_sites_Cartn_transform_axes. x' |11 12 13| x | 1 | ( y' ) fractional = |21 22 23| ( y ) Cartesian + | 2 | z' |31 32 33| z | 3 |

Category: atom_sites

Type: numb

Codes which identify the methods used to locate the initial atom sites. The *_primary code identifies how the first atom sites were determined; the *_secondary code identifies how the remaining non-hydrogen sites were located; and the *_hydrogens code identifies how the hydrogen sites were located. Ref: Sheldrick, G. M., Hauptman, H. A., Weeks, C. M., Miller, R. and Us\'on, I. (2001). Ab initio phasing. In International Tables for Crystallography, Vol. F. Crystallography of biological macromolecules, edited by M. G. Rossmann and E. Arnold, ch. 16.1. Dordrecht: Kluwer Academic Publishers.

Category: atom_sites

Type: char

Enumeration values:

difmap

vecmap

heavy

direct

geom

disper

isomor

notdet

dual

other

Additional information about the atomic coordinates not coded elsewhere in the CIF.

Category: atom_sites

Type: char

Data items in the ATOM_TYPE category record details about properties of the atoms that occupy the atom sites, such as the atomic scattering factors.

Category: category_overview

Type: null

Examples:

    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

Mass percentage of this atom type derived from chemical analysis.

Category: atom_type

Type: numb

List: yes

List reference: _atom_type_symbol

Range: [0.0:100.0]

A description of the atom(s) designated by this atom type. In most cases, this will be the element name and oxidation state of a single atom species. For disordered or nonstoichiometric structures it will describe a combination of atom species.

Category: atom_type

Type: char

List: yes

List reference: _atom_type_symbol

Examples:

deuterium

0.34Fe+0.66Ni

Total number of atoms of this atom type in the unit cell.

Category: atom_type

Type: numb

List: yes

List reference: _atom_type_symbol

Range: [0:]

Formal oxidation state of this atom type in the structure.

Category: atom_type

Type: numb

List: yes

List reference: _atom_type_symbol

Default value: 0

Range: [-8:8]

The effective intra- and intermolecular bonding radii in angstroms of this atom type.

Category: atom_type

Type: numb

Units: A

Units detail: angstroms

List: yes

List reference: _atom_type_symbol

Range: [0.0:5.0]

The Cromer-Mann scattering-factor coefficients 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

Category: atom_type

Type: numb

List: yes

List reference: _atom_type_symbol

The imaginary and real components of the anomalous-dispersion scattering factor, f'' and f', in electrons for this atom type and the radiation given in _diffrn_radiation_wavelength.

Category: atom_type

Type: numb

List: yes

List reference: _atom_type_symbol

Default value: 0.0

Reference to source of real and imaginary dispersion corrections for scattering factors used for this atom type.

Category: atom_type

Type: char

List: yes

List reference: _atom_type_symbol

Example:

International Tables Vol. IV Table 2.3.1

The bound coherent scattering length in femtometres for the atom type at the isotopic composition used for the diffraction experiment.

Category: atom_type

Type: numb

Units: fm

Units detail: femtometres

List: yes

List reference: _atom_type_symbol

Default value: 0.0

Reference to source of scattering factors or scattering lengths used for this atom type.

Category: atom_type

Type: char

List: yes

List reference: _atom_type_symbol

Example:

International Tables Vol. IV Table 2.4.6B

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.

Category: atom_type

Type: char

List: yes

List reference: _atom_type_symbol

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.

Category: atom_type

Type: char

List: yes

List mandatory: yes

Link child: _atom_site_type_symbol

Examples:

C

Cu2+

H(SDS)

dummy

FeNi

Data items in the AUDIT category record details about the creation and subsequent updating of the data block.

Category: category_overview

Type: null

Examples:

    _audit_block_code                  TOZ_1991-03-20

    _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.
    ;

A code intended to identify uniquely the current data block.

Category: audit

Type: char

Example:

TOZ_1991-03-20

The date that the data block was created. The date format is yyyy-mm-dd.

Category: audit

Type: char

Example:

1990-07-12

A description of how data were entered into the data block.

Category: audit

Type: char

Example:

spawned by the program QBEE

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.

Category: audit

Type: char

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.

Category: category_overview

Type: null

Examples:

    loop_
    _audit_author_name
    _audit_author_address
        'Fitzgerald, Paula M. D.'
    ;  Department of Biophysical Chemistry
       Merck Research Laboratories
       PO Box 2000, Ry80M203
       Rahway
       New Jersey 07065
       USA
    ;
        'Van Middlesworth, J. F.'
    ;  Department of Biophysical Chemistry
       Merck Research Laboratories
       PO Box 2000, Ry80M203
       Rahway
       New Jersey 07065
       USA
    ;

The address of an author of this data block. If there are multiple authors, _audit_author_address is looped with _audit_author_name.

Category: audit_author

Type: char

List: yes

List reference: _audit_author_name

Example:

                       Department
                        Institute
                        Street
                        City and postcode
                        COUNTRY

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).

Category: audit_author

Type: char

List: yes

List mandatory: yes

Examples:

Bleary, Percival R.

O'Neil, F.K.

Van den Bossche, G.

Yang, D.-L.

Simonov, Yu.A.

M\"uller, H.A.

Ross II, C.R.

Data items in the AUDIT_CONFORM category describe the dictionary versions against which the data names appearing in the current data block are conformant.

Category: category_overview

Type: null

Examples:

    _audit_conform_dict_name         cif_core.dic
    _audit_conform_dict_version      2.4
    _audit_conform_dict_location
          ftp://ftp.iucr.org/pub/cif_core.2.4.dic

A file name or uniform resource locator (URL) for the dictionary to which the current data block conforms.

Category: audit_conform

Type: char

List: both

List reference: _audit_conform_dict_name

The string identifying the highest-level dictionary defining data names used in this file.

Category: audit_conform

Type: char

List: both

List mandatory: yes

The version number of the dictionary to which the current data block conforms.

Category: audit_conform

Type: char

List: both

List reference: _audit_conform_dict_name

Data items in the AUDIT_CONTACT_AUTHOR category record details about the name and address of the author to be contacted concerning the contents of this data block.

Category: category_overview

Type: null

Examples:

    loop_
    _audit_contact_author_name
    _audit_contact_author_address
    _audit_contact_author_email
    _audit_contact_author_fax
    _audit_contact_author_phone
        'Fitzgerald, Paula M. D.'
    ;  Department of Biophysical Chemistry
       Merck Research Laboratories
       PO Box 2000, Ry80M203
       Rahway
       New Jersey 07065
       USA
    ;
        'paula_fitzgerald@merck.com'
        '1(908)5945510'
        '1(908)5945510'

The mailing address of the author of the data block to whom correspondence should be addressed.

Category: audit_contact_author

Type: char

Example:

                       Department
                        Institute
                        Street
                        City and postcode
                        COUNTRY

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.

Category: audit_contact_author

Type: char

Examples:

name@host.domain.country

bm@iucr.org

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.

Category: audit_contact_author

Type: char

Examples:

12(34)9477334

12()349477334

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).

Category: audit_contact_author

Type: char

Examples:

Bleary, Percival R.

O'Neil, F.K.

Van den Bossche, G.

Yang, D.-L.

Simonov, Yu.A.

M\"uller, H.A.

Ross II, C.R.

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.

Category: audit_contact_author

Type: char

Examples:

12(34)9477330

12()349477330

12(34)9477330x5543

Data items in the AUDIT_LINK category record details about the relationships between data blocks in the current CIF.

Category: category_overview

Type: null

Examples:

    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'

    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'

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.

Category: audit_link

Type: char

List: yes

List mandatory: yes

A textual description of the relationship of the referenced data block to the current one.

Category: audit_link

Type: char

List: yes

List reference: _audit_link_block_code

Data items in the CELL category record details about the crystallographic cell parameters and their measurement.

Category: category_overview

Type: null

Examples:

    _cell_length_a                     5.959(1)
    _cell_length_b                     14.956(1)
    _cell_length_c                     19.737(3)
    _cell_angle_alpha                  90
    _cell_angle_beta                   90
    _cell_angle_gamma                  90
    _cell_volume                       1759.0(3)

    _cell_measurement_temperature      293
    _cell_measurement_reflns_used      25
    _cell_measurement_theta_min        25
    _cell_measurement_theta_max        31

Unit-cell angles of the reported structure in degrees. The values of _refln_index_h, *_k, *_l must correspond to the cell defined by these values and _cell_length_a, *_b and *_c. The values of _diffrn_refln_index_h, *_k, *_l may not correspond to these values if a cell transformation took place following the measurement of the diffraction intensities. See also _diffrn_reflns_transf_matrix_.

Category: cell

Type: numb

Type conditions: esd

Units: deg

Units detail: degrees

Default value: 90.0

Range: [0.0:180.0]

The number of the formula units in the unit cell as specified by _chemical_formula_structural, _chemical_formula_moiety or _chemical_formula_sum.

Category: cell

Type: numb

Range: [1:]

Unit-cell lengths in angstroms corresponding to the structure reported. The values of _refln_index_h, *_k, *_l must correspond to the cell defined by these values and _cell_angle_ values. The values of _diffrn_refln_index_h, *_k, *_l may not correspond to these values if a cell transformation took place following the measurement of the diffraction intensities. See also _diffrn_reflns_transf_matrix_.

Category: cell

Type: numb

Type conditions: esd

Units: A

Units detail: angstroms

Range: [0.0:]

The pressure in kilopascals at which the unit-cell parameters were measured (not the pressure at which the sample was synthesized).

Category: cell

Type: numb

Type conditions: esd

Units: kPa

Units detail: kilopascals

Range: [0.0:]

Description of the radiation used to measure the unit-cell data. See also _cell_measurement_wavelength.

Category: cell

Type: char

Examples:

neutron

Cu K\a

synchrotron

The total number of reflections used to determine the unit cell. These reflections may be specified as _cell_measurement_refln_ data items.

Category: cell

Type: numb

The temperature in kelvins at which the unit-cell parameters were measured (not the temperature of synthesis).

Category: cell

Type: numb

Type conditions: esd

Units: K

Units detail: kelvin

Range: [0.0:]

The maximum and minimum theta angles of reflections used to measure the unit cell in degrees.

Category: cell

Type: numb

Units: deg

Units detail: degrees

Range: [0.0:90.0]

The wavelength in angstroms of the radiation used to measure the unit cell. If this is not specified, the wavelength is assumed to be the same as that given in _diffrn_radiation_wavelength.

Category: cell

Type: numb

Units: A

Units detail: angstroms

Range: [0.0:]

The angles defining the reciprocal cell in degrees. These are related to those 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.

Category: cell

Type: numb

Type conditions: esd

Units: deg

Units detail: degrees

Default value: 90.0

Range: [0.0:180.0]

The reciprocal-cell lengths in inverse angstroms. These are related to the real cell by: 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.

Category: cell

Type: numb

Type conditions: esd

Units: A^-1^

Units detail: reciprocal angstroms

Range: [0.0:]

A description of special aspects of the cell choice, noting possible alternative settings.

Category: cell

Type: char

Examples:

pseudo-orthorhombic

standard setting from 45 deg rotation around c

Cell volume V in angstroms cubed. V = a b c [1 - cos²(alpha) - cos²(beta) - cos²(gamma) + 2 cos(alpha) cos(beta) cos(gamma) ] ^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

Category: cell

Type: numb

Type conditions: esd

Units: A^3^

Units detail: cubic angstroms

Range: [0.0:]

Data items in the CELL_MEASUREMENT_REFLN category record details about the reflections used in the determination of the crystallographic cell parameters. The _cell_measurement_refln_ data items would in general be used only for diffractometer measurements.

Category: category_overview

Type: null

Examples:

    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 - - - -

Miller indices of a reflection used for measurement of the unit cell.

Category: cell_measurement_refln

Type: numb

List: yes

List mandatory: yes

Theta angle in degrees for the reflection used for measurement of the unit cell with the indices _cell_measurement_refln_index_.

Category: cell_measurement_refln

Type: numb

Units: deg

Units detail: degrees

List: yes

List reference: _cell_measurement_refln_index_

Range: [0.0:90.0]

Data items in the CHEMICAL category record details about 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.

Category: category_overview

Type: null

Examples:

    _chemical_name_systematic
      trans-bis(tricyclohexylphosphine)tetracarbonylmolybdenum(0)

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)

Category: chemical

Type: char

Enumeration values:

rm

ad

rmad

syn

unk

.

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.

Category: chemical

Type: char

Examples:

From Norilsk (USSR)

Extracted from the bark of Cinchona Naturalis

The enantioexcess of the bulk material from which the crystals were grown. A value of 0.0 indicates the racemate. A value of 1.0 indicates that the compound is enantiomerically pure. Enantioexcess is defined in the IUPAC Recommendations (Moss et al., 1996). The composition of the crystal and bulk must be the same. Ref: Moss G. P. et al. (1996). Basic Terminology of Stereochemistry. Pure Appl. Chem., 68, 2193-2222. http://www.chem.qmul.ac.uk/iupac/stereo/index.html

Category: chemical

Type: numb

Type conditions: esd

Units: .

Units detail: dimensionless

Range: [0.0:1.0]

The experimental technique used to determine the enantioexcess of the bulk compound.

Category: chemical

Type: char

Enumeration values:

OA

CD

EC

other

The enantioexcess of the crystal used for the diffraction study. A value of 0.0 indicates the racemate. A value of 1.0 indicates that the crystal is enantiomerically pure. Enantioexcess is defined in the IUPAC Recommendations (Moss et al., 1996). Ref: Moss G. P. et al. (1996). Basic Terminology of Stereochemistry. Pure Appl. Chem., 68, 2193-2222. http://www.chem.qmul.ac.uk/iupac/stereo/index.html

Category: chemical

Type: numb

Type conditions: esd

Units: .

Units detail: dimensionless

Range: [0.0:1.0]

The experimental technique used to determine the enantioexcess of the crystal.

Category: chemical

Type: char

Enumeration values:

CD

EC

other

The temperature in kelvins at which the crystalline solid changes to a liquid.

Category: chemical

Type: numb

Type conditions: esd

Units: K

Units detail: kelvin

Range: [0.0:]

A temperature in kelvins below which (*_lt) or above which (*_gt) the melting point (the temperature at which the crystalline solid changes to a liquid) lies. These items allow a range of temperatures to be given. _chemical_melting_point should always be used in preference to these items whenever possible.

Category: chemical

Type: numb

Units: K

Units detail: kelvin

Related item: _chemical_melting_point (alternate)

Range: [0.0:]

Trivial name by which the compound is commonly known.

Category: chemical

Type: char

Example:

1-bromoestradiol

Mineral name accepted by the International Mineralogical Association. Use only for natural minerals. See also _chemical_compound_source.

Category: chemical

Type: char

Example:

chalcopyrite

Commonly used structure-type name. Usually only applied to minerals or inorganic compounds.

Category: chemical

Type: char

Examples:

perovskite

sphalerite

A15

IUPAC or Chemical Abstracts full name of the compound.

Category: chemical

Type: char

Example:

1-bromoestra-1,3,5(10)-triene-3,17\b-diol

The optical rotation in solution of the compound is specified in the following format: '[α]^TEMP_WAVE = 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 per 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.

Category: chemical

Type: char

Example:

[\a]^25^~D~ = +108 (c = 3.42, CHCl~3~)

A free-text description of the biological properties of the material.

Category: chemical

Type: char

Examples:

              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

A free-text description of the physical properties of the material.

Category: chemical

Type: char

Examples:

air-sensitive

moisture-sensitive

hygroscopic

deliquescent

oxygen-sensitive

photo-sensitive

pyrophoric

semiconductor

ferromagnetic at low temperature

paramagnetic and thermochromic

The temperature in kelvins at which the solid decomposes.

Category: chemical

Type: numb

Type conditions: esd

Units: K

Units detail: kelvin

Range: [0.0:]

Example:

350

A temperature in kelvins below which (*_lt) or above which (*_gt) the solid is known to decompose. These items allow a range of temperatures to be given. _chemical_temperature_decomposition should always be used in preference to these items whenever possible.

Category: chemical

Type: numb

Units: K

Units detail: kelvin

Related item: _chemical_temperature_decomposition (alternate)

Range: [0.0:]

Example:

350

The temperature in kelvins at which the solid sublimes.

Category: chemical

Type: numb

Type conditions: esd

Units: K

Units detail: kelvin

Range: [0.0:]

Example:

350

A temperature in kelvins below which (*_lt) or above which (*_gt) the solid is known to sublime. These items allow a range of temperatures to be given. _chemical_temperature_sublimation should always be used in preference to these items whenever possible.

Category: chemical

Type: numb

Units: K

Units detail: kelvin

Related item: _chemical_temperature_sublimation (alternate)

Range: [0.0:]

Example:

350

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.

Category: category_overview

Type: null

Examples:

    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

The net integer charge assigned to this atom. This is the formal charge assignment normally found in chemical diagrams.

Category: chemical_conn_atom

Type: numb

List: yes

List reference: _chemical_conn_atom_type_symbol

Default value: 0

Range: [-6:6]

Examples:

1

-1

The 2D Cartesian coordinates (x,y) 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.

Category: chemical_conn_atom

Type: numb

List: yes

List reference: _chemical_conn_atom_type_symbol

Range: [0.0:1.0]

The number of connected atoms excluding terminal hydrogen atoms.

Category: chemical_conn_atom

Type: numb

List: yes

List reference: _chemical_conn_atom_type_symbol

Range: [0:]

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 will be the same as _atom_site_attached_hydrogens only if none of the hydrogen atoms appear in the _atom_site_ list.

Category: chemical_conn_atom

Type: numb

List: yes

List reference: _chemical_conn_atom_type_symbol

Range: [0:]

The chemical sequence number to be associated with this atom.

Category: chemical_conn_atom

Type: numb

List: yes

List reference: _chemical_conn_atom_type_symbol

Link children: _atom_site_chemical_conn_number _chemical_conn_bond_atom_1 _chemical_conn_bond_atom_2

Range: [1:]

A code identifying the atom type. This code must match an _atom_type_symbol code in the _atom_type_ list or be a recognizable element symbol.

Category: chemical_conn_atom

Type: char

List: yes

List mandatory: yes

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.

Category: category_overview

Type: null

Examples:

    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

Atom numbers which must match with chemical sequence numbers specified as _chemical_conn_atom_number values. These link the bond connection to the chemical numbering and atom sites.

Category: chemical_conn_bond

Type: numb

List: yes

Link parent: _chemical_conn_atom_number

Range: [1:]

The chemical bond type associated with the connection between the two sites _chemical_conn_bond_atom_1 and *_2.

Category: chemical_conn_bond

Type: char

List: yes

List reference: _chemical_conn_bond_atom_

Default value: sing

Enumeration values:

sing

doub

trip

quad

arom

poly

delo

pi

_chemical_formula_ items 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, *_structural and *_sum. For the data item *_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 *_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 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 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.

Category: category_overview

Type: null

Examples:

    _chemical_formula_moiety            'C18 H25 N O3'
    _chemical_formula_sum               'C18 H25 N O3'
    _chemical_formula_weight            303.40

    _chemical_formula_iupac      '[Mo (C O)4 (C18 H33 P)2]'
    _chemical_formula_moiety     'C40 H66 Mo O4 P2'
    _chemical_formula_structural '((C O)4 (P (C6 H11)3)2)Mo'
    _chemical_formula_sum         'C40 H66 Mo O4 P2'
    _chemical_formula_weight      768.81

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 (e.s.d.'s).

Category: chemical_formula

Type: char

Example:

Fe2.45(2)  Ni1.60(3)  S4

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.

Category: chemical_formula

Type: char

Example:

[Co Re (C12 H22 P)2 (C O)6].0.5C H3 O H

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.

Category: chemical_formula

Type: char

Examples:

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)

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 lists should not be included in this formula (see also _chemical_formula_analytical).

Category: chemical_formula

Type: char

Examples:

Ca ((Cl O3)2 O)2 (H2 O)6

(Pt (N H3)2 (C5 H7 N3 O)2) (Cl O4)2

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.

Category: chemical_formula

Type: char

Examples:

C18 H19 N7 O8 S

Formula mass in daltons. This mass should correspond to the formulae given under _chemical_formula_structural, *_iupac, *_moiety or *_sum and, together with the Z value and cell parameters, should yield the density given as _exptl_crystal_density_diffrn.

Category: chemical_formula

Type: numb

Units: Da

Units detail: daltons

Range: [1.0:]

Formula mass in daltons measured by a non-diffraction experiment.

Category: chemical_formula

Type: numb

Units: Da

Units detail: daltons

Range: [1.0:]

Data items in the CITATION category record details about the literature cited as being relevant to the contents of the data block.

Category: category_overview

Type: null

Examples:

    loop_
    _citation_id
    _citation_coordinate_linkage
    _citation_title
    _citation_country
    _citation_page_first
    _citation_page_last
    _citation_year
    _citation_journal_abbrev
    _citation_journal_volume
    _citation_journal_issue
    _citation_journal_id_ASTM
    _citation_journal_id_ISSN
    _citation_book_title
    _citation_book_publisher
    _citation_book_id_ISBN
    _citation_special_details
      primary  yes
    ; Crystallographic analysis of a complex between human
      immunodeficiency virus type 1 protease and
      acetyl-pepstatin at 2.0-Angstroms resolution.
    ;
      US  14209  14219  1990  'J. Biol. Chem.'  265  .
      HBCHA3  0021-9258  .  .  .
    ; The publication that directly relates to this coordinate
      set.
    ;
      2  no
    ; Three-dimensional structure of aspartyl-protease from
      human immunodeficiency virus HIV-1.
    ;
      UK  615  619  1989  'Nature'  337  .
      NATUAS  0028-0836  .  .  .
    ; Determination of the structure of the unliganded enzyme.
    ;
      3 no
    ; Crystallization of the aspartylprotease from human
      immunodeficiency virus, HIV-1.
    ;
      US  1919  1921  1989  'J. Biol. Chem.'  264  .
      HBCHA3  0021-9258  .  .  .
    ; Crystallization of the unliganded enzyme.
    ;

Abstract for the citation. This is used most when the citation is extracted from a bibliographic database that contains full text or abstract information.

Category: citation

Type: char

List: yes

List reference: _citation_id

The Chemical Abstracts Service (CAS) abstract identifier; relevant for journal articles.

Category: citation

Type: char

List: yes

List reference: _citation_id

The International Standard Book Number (ISBN) code assigned to the book cited; relevant for books or book chapters.

Category: citation

Type: char

List: yes

List reference: _citation_id

The name of the publisher of the citation; relevant for books or book chapters.

Category: citation

Type: char

List: yes

List reference: _citation_id

Example:

John Wiley

The location of the publisher of the citation; relevant for books or book chapters.

Category: citation

Type: char

List: yes

List reference: _citation_id

Example:

New York

The title of the book in which the citation appeared; relevant for books or book chapters.

Category: citation

Type: char

List: yes

List reference: _citation_id

_citation_coordinate_linkage states whether or not 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 creation of the data block, the value of this data item would be 'no'.

Category: citation

Type: char

List: yes

List reference: _citation_id

Enumeration values:

no

n

yes

y

The country of publication; relevant for books and book chapters.

Category: citation

Type: char

List: yes

List reference: _citation_id

Identifier ('refcode') of the database record in the Cambridge Structural Database that contains details of the cited structure.

Category: citation

Type: char

List: yes

List reference: _citation_id

Example:

LEKKUH

Accession number used by Medline to categorize a specific bibliographic entry.

Category: citation

Type: numb

List: yes

List reference: _citation_id

Range: [1:]

Example:

89064067

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.

Category: citation

Type: char

List: yes

List mandatory: yes

Link children: _citation_author_citation_id _citation_editor_citation_id

Examples:

primary

1

2

3

Abbreviated name of the journal cited as given in the Chemical Abstracts Service Source Index.

Category: citation

Type: char

List: yes

List reference: _citation_id

Example:

J. Mol. Biol.

Full name of the journal cited; relevant for journal articles.

Category: citation

Type: char

List: yes

List reference: _citation_id

Example:

Journal of Molecular Biology

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.

Category: citation

Type: char

List: yes

List reference: _citation_id

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).

Category: citation

Type: char

List: yes

List reference: _citation_id

Example:

0070

The International Standard Serial Number (ISSN) code assigned to the journal cited; relevant for journal articles.

Category: citation

Type: char

List: yes

List reference: _citation_id

Issue number of the journal cited; relevant for journal articles.

Category: citation

Type: char

List: yes

List reference: _citation_id

Example:

2

Volume number of the journal cited; relevant for journal articles.

Category: citation

Type: char

List: yes

List reference: _citation_id

Example:

174

Language in which the cited article is written.

Category: citation

Type: char

List: yes

List reference: _citation_id

Example:

German

The first and last pages of the citation; relevant for journal articles, books and book chapters.

Category: citation

Type: char

List: yes

List reference: _citation_id

A description of special aspects of the relationship of the contents of the data block to the literature item cited.

Category: citation

Type: char

List: yes

List reference: _citation_id

Examples:

                       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

The title of the citation; relevant for journal articles, books and book chapters.

Category: citation

Type: char

List: yes

List reference: _citation_id

Example:

                       Structure of diferric duck ovotransferrin at 2.35 \%A
                        resolution.

The year of the citation; relevant for journal articles, books and book chapters.

Category: citation

Type: numb

List: yes

List reference: _citation_id

Example:

1984

Data items in the CITATION_AUTHOR category record details about the authors associated with the citations in the _citation_ list.

Category: category_overview

Type: null

Examples:

    loop_
    _citation_author_citation_id
    _citation_author_name
      primary  'Fitzgerald, P.M.D.'
      primary  'McKeever, B.M.'
      primary  'Van Middlesworth, J.F.'
      primary  'Springer, J.P.'
      primary  'Heimbach, J.C.'
      primary  'Leu, C.-T.'
      primary  'Herber, W.K.'
      primary  'Dixon, R.A.F.'
      primary  'Darke, P.L.'
      2        'Navia, M.A.'
      2        'Fitzgerald, P.M.D.'
      2        'McKeever, B.M.'
      2        'Leu, C.-T.'
      2        'Heimbach, J.C.'
      2        'Herber, W.K.'
      2        'Sigal, I.S.'
      2        'Darke, P.L.'
      2        'Springer, J.P.'
      3        'McKeever, B.M.'
      3        'Navia, M.A.'
      3        'Fitzgerald, P.M.D.'
      3        'Springer, J.P.'
      3        'Leu, C.-T.'
      3        'Heimbach, J.C.'
      3        'Herber, W.K.'
      3        'Sigal, I.S.'
      3        'Darke, P.L.'

The value of _citation_author_citation_id must match an identifier specified by _citation_id in the _citation_ list.

Category: citation_author

Type: char

List: yes

List mandatory: yes

Link parent: _citation_id

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).

Category: citation_author

Type: char

List: yes

List mandatory: yes

Examples:

Bleary, Percival R.

O'Neil, F.K.

Van den Bossche, G.

Yang, D.-L.

Simonov, Yu.A.

M\"uller, H.A.

Ross II, C.R.

This data name defines the order of the author's name in the list of authors of a citation.

Category: citation_author

Type: char

List: yes

Data items in the CITATION_EDITOR category record details about the editor associated with the book or book chapter citations in the _citation_ list.

Category: category_overview

Type: null

Examples:

    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.'

The value of _citation_editor_citation_id must match an identifier specified by _citation_id in the _citation_ list.

Category: citation_editor

Type: char

List: yes

List mandatory: yes

Link parent: _citation_id

Name 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).

Category: citation_editor

Type: char

List: yes

List mandatory: yes

Examples:

Bleary, Percival R.

O'Neil, F.K.

Van den Bossche, G.

Yang, D.-L.

Simonov, Yu.A.

M\"uller, H.A.

Ross II, C.R.

This data name defines the order of the editor's name in the list of editors of a citation.

Category: citation_editor

Type: char

List: yes

Data items in the COMPUTING category record details about the computer programs used in the crystal structure analysis.

Category: category_overview

Type: null

Examples:

    _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)'

Software used in the processing of the data. Give the program or package name and a brief reference.

Category: computing

Type: char

Examples:

CAD-4 (Enraf-Nonius, 1989)

DIFDAT, SORTRF, ADDREF (Hall & Stewart, 1990)

FRODO (Jones, 1986), ORTEP (Johnson, 1965)

CRYSTALS (Watkin, 1988)

SHELX85 (Sheldrick, 1985)

Data items in the DATABASE 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 CIF if they originate from that source.

Category: category_overview

Type: null

Examples:

    _database_code_CSD                  'VOBYUG'

The codes are assigned by databases: Chemical Abstracts; Cambridge Structural Database (organic and metal-organic compounds); Inorganic Crystal Structure Database; Metals Data File (metal structures); NBS (NIST) Crystal Data Database (lattice parameters); Protein Data Bank; and the Powder Diffraction File (JCPDS/ICDD).

Category: database

Type: char

Deposition numbers assigned by the Cambridge Crystallographic Data Centre (CCDC) to files containing structural information archived by the CCDC.

Category: database

Type: char

Deposition numbers assigned by the Fachinformationszentrum Karlsruhe (FIZ) to files containing structural information archived by the Cambridge Crystallographic Data Centre (CCDC).

Category: database

Type: char

Deposition numbers assigned by various journals to files containing structural information archived by the Cambridge Crystallographic Data Centre (CCDC).

Category: database

Type: char

A history of changes made by the Cambridge Crystallographic Data Centre and incorporated into the Cambridge Structural Database (CSD).

Category: database

Type: char

The ASTM CODEN designator for a journal as given in the Chemical Source List maintained by the Chemical Abstracts Service, and the journal code used in the Cambridge Structural Database.

Category: database

Type: char

Data items in the DIFFRN category record details about the intensity measurements.

Category: category_overview

Type: null

Examples:

    _diffrn_special_details
    ; \q scan width (1.0 + 0.14tan\q)\%, \q scan rate
      1.2\% min^-1^. Background counts for 5 s on each side
      every scan.
    ;

    _diffrn_ambient_temperature         293

The gas or liquid surrounding the sample, if not air.

Category: diffrn

Type: char

Examples:

He

vacuum

mother liquor

The mean hydrostatic pressure in kilopascals at which the intensities were measured.

Category: diffrn

Type: numb

Type conditions: esd

Units: kPa

Units detail: kilopascals

Range: [0.0:]

The mean hydrostatic pressure in kilopascals above which (*_gt) or below which (*_lt) the intensities were measured. These items allow for a pressure range to be given. _diffrn_ambient_pressure should always be used in preference to these items whenever possible.

Category: diffrn

Type: numb

Units: kPa

Units detail: kilopascals

Related item: _diffrn_ambient_pressure (alternate)

Range: [0.0:]

The mean temperature in kelvins at which the intensities were measured.

Category: diffrn

Type: numb

Type conditions: esd

Units: K

Units detail: kelvin

Range: [0.0:]

The mean temperature in kelvins above which (*_gt) or below which (*_lt) the intensities were measured. These items allow a range of temperatures to be given. _diffrn_ambient_temperature should always be used in preference to these items whenever possible.

Category: diffrn

Type: numb

Units: K

Units detail: kelvin

Related item: _diffrn_ambient_temperature (alternate)

Range: [0.0:]

Remarks about how the crystal was treated prior to the intensity measurements. Particularly relevant when intensities were measured at low temperature.

Category: diffrn

Type: char

Examples:

equilibrated in hutch for 24 hours

flash frozen in liquid nitrogen

slow cooled with direct air stream

Fraction of unique (symmetry-independent) reflections measured out to _diffrn_reflns_theta_full.

Category: diffrn

Type: numb

Range: [0:1.0]

Fraction of unique (symmetry-independent) reflections measured out to _diffrn_reflns_theta_max.

Category: diffrn

Type: numb

Range: [0:1.0]

Special details of the intensity-measurement process. Should include information about source instability, crystal motion, degradation and so on.

Category: diffrn

Type: char

Example:

              The results may not be entirely reliable
               as the measurement was made during a heat
               wave when the air-conditioning had failed.

Observed diffraction point symmetry, systematic absences and possible space group(s) or superspace group(s) compatible with these.

Category: diffrn

Type: char

Data items in the DIFFRN_ATTENUATOR category record details about the diffraction attenuator scales employed.

Category: category_overview

Type: null

Examples:

      loop_
        _diffrn_attenuator_code
        _diffrn_attenuator_scale       
            0         1.00
            1        16.97
            2        33.89

A code associated with a particular attenuator setting. This code is referenced by the _diffrn_refln_attenuator_code which is stored with the intensities. See _diffrn_attenuator_scale.

Category: diffrn_attenuator

Type: char

List: yes

List mandatory: yes

Link child: _diffrn_refln_attenuator_code

Material from which the attenuator is made.

Category: diffrn_attenuator

Type: char

List: yes

List reference: _diffrn_attenuator_code

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.

Category: diffrn_attenuator

Type: numb

List: yes

List reference: _diffrn_attenuator_code

Range: [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.

Category: category_overview

Type: null

Examples:

    _diffrn_detector                    'multiwire'
    _diffrn_detector_type               'Siemens'

The general class of the radiation detector.

Category: diffrn_detector

Type: char

Related item: _diffrn_radiation_detector (alternate)

Examples:

photographic film

scintillation counter

CCD plate

BF~3~ counter

The resolution of an area detector, in pixels/mm.

Category: diffrn_detector

Type: numb

Units: mm^-1^

Units detail: pixels per millimetre

Range: [0.0:]

A description of special aspects of the radiation detector.

Category: diffrn_detector

Type: char

The deadtime in microseconds of the detector used to measure the diffraction intensities.

Category: diffrn_detector

Type: numb

Related item: _diffrn_radiation_detector_dtime (alternate)

Range: [0.0:]

The make, model or name of the detector device used.

Category: diffrn_detector

Type: char

The detector used to measure the diffraction intensities.

Category: diffrn_detector

Type: char

Related item: _diffrn_detector (replace)

The deadtime in microseconds of the detector used to measure the diffraction intensities.

Category: diffrn_detector

Type: numb

Related item: _diffrn_detector_dtime (replace)

Range: [0.0:]

Data items in the DIFFRN_MEASUREMENT category refer to the mounting of the sample and to the goniometer on which it is mounted.

Category: category_overview

Type: null

Examples:

    _diffrn_measurement_device_type
                              'Philips PW1100/20 diffractometer'
    _diffrn_measurement_method          \q/2\q

A description of special aspects of the intensity measurement.

Category: diffrn_measurement

Type: char

Example:

440 frames of 0.25\%

The general class of goniometer or device used to support and orient the specimen.

Category: diffrn_measurement

Type: char

Examples:

three-circle diffractometer

four-circle diffractometer

\k-geometry diffractometer

oscillation camera

precession camera

A description of special aspects of the device used to measure the diffraction intensities.

Category: diffrn_measurement

Type: char

Example:

                                commercial goniometer modified locally to
                                 allow for 90\% \t arc

The make, model or name of the measurement device (goniometer) used.

Category: diffrn_measurement

Type: char

Method used to measure the intensities.

Category: diffrn_measurement

Type: char

Example:

profile data from \q/2\q scans

The physical device used to support the crystal during data collection.

Category: diffrn_measurement

Type: char

Examples:

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 intensities.

Category: category_overview

Type: null

Examples:

    _diffrn_orient_matrix_UB_11           -0.04170
    _diffrn_orient_matrix_UB_12           -0.01429
    _diffrn_orient_matrix_UB_13           -0.02226
    _diffrn_orient_matrix_UB_21           -0.00380
    _diffrn_orient_matrix_UB_22           -0.05578
    _diffrn_orient_matrix_UB_23           -0.05048
    _diffrn_orient_matrix_UB_31            0.00587
    _diffrn_orient_matrix_UB_32           -0.13766
    _diffrn_orient_matrix_UB_33            0.02277

    _diffrn_orient_matrix_type 'TEXSAN convention (MSC, 1989)'

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.

Category: diffrn_orient_matrix

Type: char

The elements of the diffractometer orientation matrix. These define the dimensions of the reciprocal cell and its orientation to the local diffractometer axes. See _diffrn_orient_matrix_type.

Category: diffrn_orient_matrix

Type: numb

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.

Category: category_overview

Type: null

Examples:

    loop_
    _diffrn_orient_refln_index_h
    _diffrn_orient_refln_index_k
    _diffrn_orient_refln_index_l
    _diffrn_orient_refln_angle_theta
    _diffrn_orient_refln_angle_phi
    _diffrn_orient_refln_angle_omega
    _diffrn_orient_refln_angle_kappa
      -3   2   3    7.35   44.74   2.62    17.53
      -4   1   0    9.26   83.27   8.06     5.79
       0   0   6    5.85  -43.93 -25.36    86.20
       2   1   3    7.36  -57.87   6.26     5.42
       0   0  -6    5.85 -161.59  36.96   -86.79
      -3   1   0    6.74   80.28   5.87     2.60
       2   0   3    5.86  -76.86  -0.17    21.34
       0   0  12   11.78  -44.02 -19.51    86.41
       0   0 -12   11.78 -161.67  42.81   -86.61
      -5   1   0   11.75   86.24   9.16     7.44
       0   4   6   11.82  -19.82  10.45     4.19
       5   0   6   14.13  -77.28  10.17    15.34
       8   0   0   20.79  -77.08  25.30   -13.96

Diffractometer angles of a reflection used to define the orientation matrix in degrees. See _diffrn_orient_matrix_UB_ and _diffrn_orient_refln_index_h, *_k and *_l.

Category: diffrn_orient_refln

Type: numb

Units: deg

Units detail: degrees

List: yes

List reference: _diffrn_orient_refln_index_

The indices of a reflection used to define the orientation matrix. See _diffrn_orient_matrix_.

Category: diffrn_orient_refln

Type: numb

List: yes

List mandatory: yes

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.

Category: category_overview

Type: null

Examples:

    _diffrn_radiation_type             'Cu K\a'
    _diffrn_radiation_monochromator    'graphite'

The collimation or focusing applied to the radiation.

Category: diffrn_radiation

Type: char

Examples:

0.3 mm double-pinhole

0.5 mm

focusing mirrors

Absorption edge in angstroms of the radiation filter used.

Category: diffrn_radiation

Type: numb

Units: A

Units detail: angstroms

Range: [0.0:]

Half-width in millimetres of the incident beam in the direction perpendicular to the diffraction plane.

Category: diffrn_radiation

Type: numb

Range: [0.0:]

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.

Category: diffrn_radiation

Type: char

Examples:

Zr filter

Ge 220

none

equatorial mounted graphite

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.

Category: diffrn_radiation

Type: numb

Units: deg

Units detail: degrees

Range: [-180.0:180.0]

Polarization ratio of the diffraction beam incident on the crystal. It is the ratio of the perpendicularly polarized to the parallel polarized components 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).

Category: diffrn_radiation

Type: numb

Range: [0.0:]

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 be given, so that the probe radiation can be simply determined.

Category: diffrn_radiation

Type: char

Enumeration values:

x-ray

neutron

electron

gamma

The type of the radiation. This is used to give a more detailed description than _diffrn_radiation_probe and is typically a description of the X-ray wavelength in Siegbahn notation.

Category: diffrn_radiation

Type: char

Examples:

Cu K\a

Cu K\a~1~

Cu K-L~2,3~

white-beam

The IUPAC symbol for the X-ray wavelength for the probe radiation.

Category: diffrn_radiation

Type: char

Enumeration values:

K-L~3~

K-L~2~

K-M~3~

K-L~2,3~

Data items in the DIFFRN_RADIATION_WAVELENGTH category describe the wavelength of the radiation used in measuring the diffraction intensities. Items may be looped to identify and assign weights to distinct wavelength components from a polychromatic beam.

Category: category_overview

Type: null

Examples:

    _diffrn_radiation_wavelength       1.5418

The radiation wavelength in angstroms.

Category: diffrn_radiation_wavelength

Type: numb

Units: A

Units detail: angstroms

List: both

List reference: _diffrn_radiation_wavelength_id

Range: [0.0:]

An arbitrary code identifying each value of _diffrn_radiation_wavelength. Items in the DIFFRN_RADIATION category are looped when multiple wavelengths are used. This code is used to link with the _diffrn_refln_ list. It must match with one of the _diffrn_refln_wavelength_id codes.

Category: diffrn_radiation_wavelength

Type: char

List: yes

List mandatory: yes

Link child: _diffrn_refln_wavelength_id

Examples:

x1

x2

neut

The relative weight of a wavelength identified by the code _diffrn_radiation_wavelength_id in the list of wavelengths.

Category: diffrn_radiation_wavelength

Type: numb

List: yes

List reference: _diffrn_radiation_wavelength_id

Default value: 1.0

Range: [0.0:1.0]

Data items in the DIFFRN_REFLN category record details about the 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. The DIFFRN_REFLNS data items are not looped.)

Category: category_overview

Type: null

Examples:

    loop_
        _diffrn_refln_index_h
        _diffrn_refln_index_k
        _diffrn_refln_index_l
        _diffrn_refln_angle_chi
        _diffrn_refln_scan_rate
        _diffrn_refln_counts_bg_1
        _diffrn_refln_counts_total
        _diffrn_refln_counts_bg_2
        _diffrn_refln_angle_theta
        _diffrn_refln_angle_phi
        _diffrn_refln_angle_omega
        _diffrn_refln_angle_kappa
        _diffrn_refln_scan_width
        _diffrn_refln_elapsed_time

 0  0 -16  0. 4.12  28 127  36  33.157  -75.846  16.404   50.170  1.516 19.43
 0  0 -15  0. 4.12  38 143  28  30.847  -75.846  14.094   50.170  1.516 19.82
 0  0 -14  0. 1.03 142 742 130  28.592  -75.846  11.839   50.170  1.516 21.32
 0  0 -13  0. 4.12  26 120  37  26.384  -75.846   9.631   50.170  1.450 21.68
 0  0 -12  0. 0.97 129 618 153  24.218  -75.846   7.464   50.170  1.450 23.20
 0  0 -11  0. 4.12  33 107  38  22.087  -75.846   5.334   50.170  1.384 23.55
 0  0 -10  0. 4.12  37 146  33  19.989  -75.846   3.235   50.170  1.384 23.90
 0  0  -9  0. 4.12  50 179  49  17.918  -75.846   1.164   50.170  1.384 24.25
    # - - - - data truncated for brevity - - - -
 3  4  -4  0. 1.03  69 459  73  30.726  -53.744  46.543  -47.552  1.516 2082.58
 3  4  -5  0. 1.03  91 465  75  31.407  -54.811  45.519  -42.705  1.516 2084.07
 3 14  -6  0. 1.03  84 560  79  32.228  -55.841  44.745  -38.092  1.516 2085.57
    # - - - - data truncated for brevity - - - -

The diffractometer angles of a reflection in degrees. These correspond to the specified orientation matrix and the original measured cell before any subsequent cell transformations.

Category: diffrn_refln

Type: numb

Units: deg

Units detail: degrees

List: yes

List reference: _diffrn_refln_index_

The code identifying the attenuator setting for this reflection. This code must match one of the _diffrn_attenuator_code values.

Category: diffrn_refln

Type: char

List: yes

List reference: _diffrn_refln_index_

Link parent: _diffrn_attenuator_code

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|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_refln

Type: char

List: yes

List reference: _diffrn_refln_index_

Link parent: _diffrn_reflns_class_code

The diffractometer counts for the measurements: background before the peak, background after the peak, net counts after background removed, counts for peak scan or position, and the total counts (background plus peak).

Category: diffrn_refln

Type: numb

List: yes

List reference: _diffrn_refln_index_

Code identifying each crystal if multiple crystals are used. Is used to link with _exptl_crystal_id in the _exptl_crystal_ list.

Category: diffrn_refln

Type: char

List: yes

List reference: _diffrn_refln_index_

Link parent: _exptl_crystal_id

Total slit apertures in degrees in the diffraction plane (*_horiz) and perpendicular to the diffraction plane (*_vert).

Category: diffrn_refln

Type: numb

Units: deg

Units detail: degrees

List: yes

List reference: _diffrn_refln_index_

Range: [0.0:90.0]

Elapsed time in minutes from the start of the diffraction experiment to the measurement of this intensity.

Category: diffrn_refln

Type: numb

Units: min

Units detail: minutes

List: yes

List reference: _diffrn_refln_index_

Range: [0.0:]

Miller indices of a measured reflection. These need not match the _refln_index_h, *_k, *_l values 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_.

Category: diffrn_refln

Type: numb

List: yes

List mandatory: yes

Net intensity calculated from the diffraction counts after the attenuator and standard scales have been applied.

Category: diffrn_refln

Type: numb

List: yes

List reference: _diffrn_refln_index_

Range: [0:]

Standard uncertainty (e.s.d.) of the net intensity calculated from the diffraction counts after the attenuator and standard scales have been applied.

Category: diffrn_refln

Type: numb

List: yes

List reference: _diffrn_refln_index_

Related item: _diffrn_refln_intensity_u (replace)

Range: [0:]

Standard uncertainty of the net intensity calculated from the diffraction counts after the attenuator and standard scales have been applied.

Category: diffrn_refln

Type: numb

List: yes

List reference: _diffrn_refln_index_

Related item: _diffrn_refln_intensity_sigma (alternate)

Range: [0:]

The code identifying the scale applicable to this reflection. This code must match with a specified _diffrn_scale_group_code value.

Category: diffrn_refln

Type: char

List: yes

List reference: _diffrn_refln_index_

Link parent: _diffrn_scale_group_code

The code identifying the mode of scanning for measurements using a diffractometer. See _diffrn_refln_scan_width and _diffrn_refln_scan_mode_backgd.

Category: diffrn_refln

Type: char

List: yes

List reference: _diffrn_refln_index_

Enumeration values:

om

ot

q

The code identifying the mode of scanning a reflection to measure the background intensity.

Category: diffrn_refln

Type: char

List: yes

List reference: _diffrn_refln_index_

Enumeration values:

st

mo

The rate of scanning a reflection in degrees per minute to measure the intensity.

Category: diffrn_refln

Type: numb

Units: deg/min

Units detail: degrees per minute

List: yes

List reference: _diffrn_refln_index_

Range: [0.0:]

The time spent measuring each background in seconds.

Category: diffrn_refln

Type: numb

Units: sec

Units detail: seconds

List: yes

List reference: _diffrn_refln_index_

Range: [0.0:]

The scan width in degrees of the scan mode defined by the code _diffrn_refln_scan_mode.

Category: diffrn_refln

Type: numb

Units: deg

Units detail: degrees

List: yes

List reference: _diffrn_refln_index_

Range: [0.0:90.0]

The (sin theta)/lambda value in reciprocal angstroms for this reflection.

Category: diffrn_refln

Type: numb

Units: A^-1^

Units detail: reciprocal angstroms

List: yes

List reference: _diffrn_refln_index_

Range: [0.0:]

A code indicating that this reflection was measured as a standard reflection. The value must be '.' or match one of the _diffrn_standard_refln_code values.

Category: diffrn_refln

Type: char

List: yes

List reference: _diffrn_refln_index_

Link parent: _diffrn_standard_refln_code

Examples:

1

2

3

s1

s2

s3

A

B

C

The mean wavelength in angstroms of the radiation used to measure the intensity of this reflection. This is an important parameter for reflections measured using energy-dispersive detectors or the Laue method.

Category: diffrn_refln

Type: numb

Units: A

Units detail: angstroms

List: yes

List reference: _diffrn_refln_index_

Range: [0.0:]

Code identifying the wavelength in the _diffrn_radiation_ list.

Category: diffrn_refln

Type: char

List: yes

List reference: _diffrn_refln_index_

Link parent: _diffrn_radiation_wavelength_id

Examples:

x1

x2

neut

Data items in the DIFFRN_REFLNS category record details about the set of intensities measured in the diffraction experiment. The DIFFRN_REFLNS data items specify the parameters that apply to all intensity measurements. The DIFFRN_REFLNS data items are not looped. (The DIFFRN_REFLN data items refer to individual intensity measurements and must be included in looped lists.)

Category: category_overview

Type: null

Examples:

    _diffrn_reflns_number              1592
    _diffrn_reflns_av_R_equivalents    0
    _diffrn_reflns_av_unetI/netI       .027
    _diffrn_reflns_limit_h_min         0
    _diffrn_reflns_limit_h_max         6
    _diffrn_reflns_limit_k_min        -17
    _diffrn_reflns_limit_k_max         0
    _diffrn_reflns_limit_l_min         0
    _diffrn_reflns_limit_l_max         22
    _diffrn_reflns_theta_min           3.71
    _diffrn_reflns_theta_max           61.97

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 symmetry-equivalent intensities.

Category: diffrn_reflns

Type: numb

Range: [0.0:]

Measure [sum |u(net I)|/sum|net I|] for all measured reflections.

Category: diffrn_reflns

Type: numb

Related item: _diffrn_reflns_av_unetI/netI (replace)

Range: [0.0:]

Measure [sum |u(net I)|/sum|net I|] for all measured reflections.

Category: diffrn_reflns

Type: numb

Related item: _diffrn_reflns_av_sigmaI/netI (alternate)

Range: [0.0:]

Fraction of Laue unique reflections (symmetry-independent in the Laue group) measured out to the resolution given in _diffrn_reflns_resolution_full or _diffrn_reflns_theta_full. The Laue group always contains a centre of symmetry so that the reflection h,k,l is always equivalent to the reflection -h,-k,-l even in space groups without a centre of symmetry. This number should not be less than 0.95, since it represents the fraction of reflections measured in the part of the diffraction pattern that is essentially complete.

Category: diffrn_reflns

Type: numb

Related item: _diffrn_measured_fraction_theta_full (alternate)

Range: [0.95:1.0]