data requirements for structures
A list of all data items required in a submitted CIF is available from the online CIF help page. Authors are required to validate each CIF and associated structure factors prior to submission by using the checkCIF service at http://journals.iucr.org/services/cif/checking/checkfull.html (see Notes for Authors §2.1 and §2.3).
All validation alerts returned by checkCIF should be considered carefully and corrected as far as possible. Often the minor alerts point to easily fixed oversights, errors or omissions in the CIF or refinement strategy. In order to resolve some of the more serious items it may be necessary to carry out additional measurements or structure refinements. However, the nature of the study might justify the reported deviations from the checkCIF criteria and in such cases these should be commented upon in the paper. If level A alerts remain and are believed to be justified or unavoidable deviations, the validation response form (VRF) supplied by checkCIF should be completed and included in the submitted CIF, preferably with the addition of appropriate explanatory text in the published experimental section of the CIF. A completed VRF will look something like:
# start Validation Reply Form _vrf_CHEMW03_6 ; PROBLEM: The ratio of given/expected molecular weight as calculated from the _atom_site* data lies outside... RESPONSE: SQUEEZE used to remove disordered diethyl ether solvent molecule, but the reported formula includes the solvent. See _refine_special_details. ; # end Validation Reply Form
At the time of submission, if the CIF is incomplete, has a syntax problem or generates validation A alerts and there is no corresponding validation response form (VRF) in the CIF, the submission process will not proceed to the next step until these matters are rectified.
A commented list of some of the more important data requirements are summarized below and a more complete description of the data-validation checks applied to submitted CIFs is available from the online CIF help page.
The chemical formula must be consistent with the atomic content specified by the _atom_site_ information, and match the _chemical_formula_weight. If atoms are missing from the atomic model (e.g. unlocated H atoms or solvent molecules suppressed by the 'SQUEEZE' or similar approach), the moiety and sum formulae should state the assumed overall formula.
The space group must encompass the highest symmetry permitted by the diffraction intensities and be consistent with the _cell_length_ and _cell_angle_ values.
The number of formula units in the unit cell must comply with that expected from the chemical formula, the space group and the _atom_site_ data.
The crystal colour should comply with the codes listed in the online CIF help page.
Authors are encouraged to use crystals no larger than the incident X-ray beam diameter, particularly when heavy or strongly absorbing elements are present in the material. For best results, the crystal should be uniformly bathed in the X-ray beam. The size of the beam at the crystal is normally determined by inter alia the nature of the X-ray source and the beam optics. Note that with fine-focus sealed X-ray tubes, the use of a collimator larger than the filament diameter does not automatically increase the size of the uniform part of the incident beam.
Permitted absorption-type codes are listed in the online CIF help page. A type code must be accompanied by a reference to the method or the software used; this should be given in the field _exptl_absorpt_process_details. The need for absorption corrections, and the appropriate type of correction, is dependent on the value, _exptl_absorpt_coefficient_mu, and the crystal size values, _exptl_crystal_size_min, _mid and _max. If x is the medial size _mid, the product x provides an indication of the type of correction needed. Analytical or numerical corrections may be beneficial if x exceeds 1.0 and are strongly recommended if x is above 3.0. However, corrections based on analyses of equivalent and redundant reflections (multi-scan methods) are acceptable. Corrections are usually unnecessary if x is below 0.1. Refined absorption methods are discouraged except in special circumstances. The experimentally determined transmission-factor limits _exptl_absorpt_correction_T_min and _max should be consistent with those expected for the crystal shape and size, and. Whenever a multi-scan type absorption correction is being employed (e.g. by using SADABS), authors are also encouraged to measure a multiplicity of observations (measurement of symmetry equivalents or the same reflection at different crystal orientations) of at least 4. The algorithms used in such programs work best and produce the highest quality data only when the multiplicity of observations or coverage of the full sphere of reflections is high.
These items should refer to the complete set of measured data before any merging of symmetry-equivalent reflections, and not only to the unique set of data.
The number of symmetry-independent reflections excludes the systematically extinct intensities. Authors are encouraged to use all symmetry-independent reflections in the refinement of the structure parameters.
This threshold, which is based on multiples of I, F2 or F, serves to identify the 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. The multiplier in the threshold expression should be as small as possible, typically 2 or less.
The max of measured reflections should be such that sin max/ exceeds 0.6 Å-1 (i.e. max > 25° for Mo K; max > 67° for Cu K). It is expected that all possible unique reflections out to at least the specified minimum limits are measured. This provides the minimum number of reflections recommended for an average structural study. If intensities are consistently weak at the recommended max, low-temperature measurements may be needed unless a study at a specific temperature (or pressure) is being reported.
This is the fraction of unique (symmetry-independent) reflections measured out to _diffrn_reflns_theta_max. Ideally, this should be as close to 1.0 as possible.
When _diffrn_measured_fraction_theta_max is less than 1.0 because of some missing high-angle reflections, full is the diffractometer angle at which the measured reflection count is close to complete. The fraction of unique reflections measured out to this angle is given by _diffrn_measured_fraction_theta_full.
Sufficient symmetry-equivalent reflections must be measured to provide a good estimate of the intensity reproducibility. This is particularly important when absorption corrections are applied (this value is calculated after the corrections are applied to the intensities). See also _exptl_absorpt_correction_type.
Note that this value is not intended as a reliable gauge of structure precision which is better determined from the standard uncertainties of the parameters (these depend on the number and reliability of the measured structure factors used in the refinement process).
The number of reflections used in the refinement should be as large as possible, and should, if possible, be greater than the number of refined parameters _refine_ls_number_parameters by at least a factor of 10 if the structure is centrosymmetric, or by a factor of 8 if it is not. Omission of outlier reflections should be avoided unless there is good reason and, in such cases, details of the omitted reflections and the reasons for doing so should be included in the _publ_section_exptl_refinement section.
This is the number of coordinate, atomic displacement, scale, occupancy, restraint, extinction and other parameters refined independently in the least-squares process. It is possible, and sometimes desirable, to reduce this number by the appropriate application of geometric constraints.
This gives the number of applied restraints. Concise details of what these restraints were, including any target values applied and the effective standard deviation of the restraint, should be included in the _publ_section_exptl_refinement section of the CIF.
The codes which identify the treatment of H-atom parameters are listed in the online CIF help page. When special procedures for locating and refining H atoms have been employed, details about the treatment of H-atom sites should be placed in _publ_section_exptl_refinement. Authors should note the advice on H-atom treatment given in the SHELXL97 manual , §4.6: `For most purposes it is preferable to calculate the hydrogen positions according to well-established geometrical criteria and then adopt a refinement procedure which ensures that a sensible geometry is retained'. Authors should note that H-atom sites which have been fixed or constrained by geometry (e.g. riding) will not have s.u. values associated with them.
Weighting schemes for refinements should be based on the standard uncertainties in the measured reflection data.
This is the largest ratio of the parameter shift to standard uncertainty after the final round of refinement and is typically within ±0.01 if sufficient least-squares refinement cycles have been employed. A value above ±0.05 is considered unusual and values beyond ±0.1 are a sign of incomplete refinement, unaccounted-for disorder or high correlation between parameters that should be constrained. Authors should explain the reasons for a high value in _publ_section_exptl_refinement.
These values are expected to be small, especially for light-atom structures. If their magnitudes are such that a validation alert is generated, the label and the distance of the closest atom site should be reported in _publ_section_exptl_refinement.
All geometry values must originate from the submitted _atom_site_fract_ values. Only geometry values of significance to the structure will be published. These must be identified with a _geom_..._flag value of yes in the submitted CIF. Note that dimensions involving H-atom sites which have been fixed or constrained by geometry will not have s.u. values associated with them. Details of all bond lengths and angles involving H atoms must be included in the CIF, even if they have been constrained.
See also Tips for finalizing refinement.
Atomic coordinates for molecular and the unique part of extended species should be supplied as connected sets. Whenever structure geometry permits, it is good practice to choose the set of connected coordinates which specify the asymmetric unit to have their centre of gravity within the primary unit cell. In systems with hydrogen-bonded networks, it is helpful to choose the asymmetric unit so that the minimum number of symmetry operators is required to specify the hydrogen-bond network. Among other things, these concepts help simplify the labelling of packing diagrams.
Values of _atom_site_occupancy should be 1.0 except for disordered or non-stoichiometric atom sites. Atom sites constrained to model disorder must be indicated by _atom_site_disorder_group. The overall packing in the structure will be checked for significant vacant regions (i.e. voids) indicating omitted solvent molecules. Deliberately omitted solvent molecules should be documented in the Comment or _publ_section_exptl_refinement sections. Note that s.u. values should not be appended to parameters which are fixed by symmetry, geometry or other constraints.
Checks will be made for non-positive-definite anisotropic atomic displacement parameters. The ratio of maximum to minimum eigenvalues should not, except in special circumstances (e.g. disorder), exceed 5.
This item should describe the method applied, with a literature citation if necessary, and the number of Friedel pairs used in the determination of the absolute structure parameter. Absolute structure is relevant in any non-centrosymmetric space group. Authors should be aware of the difference between absolute structure and absolute configuration. To improve the precision of the absolute structure parameter, the use of a large fraction of the complete set of Friedel pairs in the data set is strongly recommended. When the precision of the absolute structure parameter renders the analysis inconclusive, it is not necessary to merge Friedel-pair reflections, but if authors do merge Friedel-pair reflections before final refinement, they should mention that fact in the _publ_section_exptl_refinement section and not report a value for the Flack parameter in the CIF. Useful articles on this topic by Flack & Bernardinelli [Acta Cryst. (1999), A55, 908-915; J. Appl. Cryst. (2000), 33, 1143-1148] and Flack, Sadki, Thompson & Watkin [Acta Cryst. (2011), A67, 21-34] discuss the use, meaning and significance of the Flack parameter and its s.u. value. For pertinent comments on the determination of absolute structure, authors are also referred to the articles by Jones [Acta Cryst. (1986), A42, 57], Hooft et al. [J. Appl. Cryst. (2008), 41, 96-103; J. Appl. Cryst. (2010), 43, 665-668] and Parsons & Flack [Acta Cryst. (2004), A60, s61].