International
Tables for
Crystallography
Volume G
Definition and exchange of crystallographic data
Edited by S. R. Hall and B. McMahon

International Tables for Crystallography (2006). Vol. G, ch. 3.2, pp. 92-98

Section 3.2.2. Experimental measurements

S. R. Hall,a* P. M. D. Fitzgeraldb and B. McMahonc

aSchool of Biomedical and Chemical Sciences, University of Western Australia, Crawley, 6009, Australia,bMerck Research Laboratories, Rahway, New Jersey, USA, and cInternational Union of Crystallography, 5 Abbey Square, Chester CH1 2HU, England
Correspondence e-mail:  syd@crystal.uwa.edu.au

3.2.2. Experimental measurements

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Crystallographic archive files predating CIF were often constructed to serve the purposes of a particular software program or suite and stored the data generated by an experiment without providing a full record of the conditions under which the data were obtained. This is not unique to crystallography: many data formats make no provision for the metadata – information about the procedures for gathering and analysing data – that give context and in many cases significance to the numeric values. A specific goal of the design of CIF was to treat such supporting information as essential elements of the whole collection of information relating to a structure determination, rather than as optional and poorly defined metadata. There are therefore many categories in the core dictionary that relate to experimental conditions and apparatus, and these categories are discussed in this section. They include the categories in the DIFFRN group describing the traditional crystallographic diffraction experiment (typically a single-crystal laboratory-based X-ray determination, but increasingly including synchrotron experiments and experiments using other radiation types). There are also categories that describe and characterize the crystal used in the experiment and those that characterize the unit cell, since the experimental determination of the cell parameters is an essential part of the full structure-determination experiment.

3.2.2.1. Crystal cell parameters and measurement conditions

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The categories describing the crystal unit cell and its determination are as follows:

CELL group
 CELL
 CELL_MEASUREMENT_REFLN

The data items in these categories are as follows:

(a) CELL [Scheme scheme1]

(b) CELL_MEASUREMENT_REFLN [Scheme scheme2]

The bullet ([\bullet]) indicates a category key.

The CELL category includes two groups of data names: those characterizing a crystal unit cell, and those describing the experimental conditions relating to the unit-cell determination. It is a feature of the formal definition of the category classification unit in CIF dictionaries that these may be classed within the same category, whereas the Miller indices of the reflections used in the measurement of the unit cell belong to a different category. An argument could be made for dividing the CELL category into two categories to reflect the division drawn above between the cell parameters and their determination. However, the CIF dictionaries have been designed to have as few separate categories as possible, subject to the constraint that data items that are looped together in the same list must belong to the same category.

The individual dictionary definitions of the data items in this category are unambiguous, with the possible exception of _cell_formula_units_Z, which records the number of complete chemical formula units present in the unit cell, and not the number of repetitions of the asymmetric unit. In some instances the value of Z could be less than the number of repetitions of the asymmetric unit, such as when an internally symmetric molecular unit is positioned on a symmetry element and spans multiple asymmetric units. Of course, Z can be greater than the number of repetitions of the asymmetric unit (i.e. [Z'>1]).

Note that the value associated with the data item _cell_volume is not independent, but can be derived from the other cell parameters. Within the core dictionary there are many cases of derivable items, both because they have traditionally been reported separately and because the presence of redundant information allows cross checking of the internal consistency of the data set.

Data items in the CELL_MEASUREMENT_REFLN category record details about the reflections used to determine the crystallographic cell parameters. The key items in this list are marked with bullets; all three of the h, k, l values are needed to identify a reflection.

3.2.2.2. Data collection

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The categories describing data collection are as follows:

DIFFRN group
General description (§3.2.2.2.1[link])
 DIFFRN
Apparatus and instrumentation before the crystal (§3.2.2.2.2[link])
 DIFFRN_ATTENUATOR
 DIFFRN_RADIATION
 DIFFRN_RADIATION_WAVELENGTH
 DIFFRN_SOURCE
Apparatus and instrumentation at the crystal (§3.2.2.2.3[link])
 DIFFRN_MEASUREMENT
 DIFFRN_ORIENT_MATRIX
 DIFFRN_ORIENT_REFLN
Apparatus and instrumentation after the crystal (§3.2.2.2.4[link])
 DIFFRN_DETECTOR
Intensity measurements (§3.2.2.2.5[link])
 DIFFRN_REFLN
 DIFFRN_REFLNS
 DIFFRN_REFLNS_CLASS
 DIFFRN_SCALE_GROUP
 DIFFRN_STANDARD_REFLN
 DIFFRN_STANDARDS

The category group related to the diffraction experiment is broad and includes details of the apparatus as well as the measurements. The individual categories are grouped together according to location within the experimental setup (see Fig. 3.2.2.1[link]) or the measurement of intensities.

[Figure 3.2.2.1]

Figure 3.2.2.1 | top | pdf |

Scheme of a diffraction experiment.

3.2.2.2.1. General description

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The data items in this category are as follows:

DIFFRN [Scheme scheme3]

These data items give an overview of the diffraction experiment. They are intended to be independent of the instrument, techniques or methodology of the experiment.

The items describing the ambient environmental conditions are reasonably self-explanatory. They are often absent from a CIF, because an author has not thought it necessary to provide information for experiments conducted under `normal' conditions of room temperature and pressure, and in a standard atmosphere. However, `normal room temperature' may span a range of many degrees Kelvin and might have a non-negligible effect upon cell dimension measurements, so the temperature should be given. As there is significant variability in the ambient temperature at which laboratory experiments may be carried out, it is not appropriate to assign a default value for _diffrn_ambient_temperature, since any numeric value chosen as a default could be misconstrued as an experimentally determined value. If the ambient temperature has not been measured, an author may supply a best estimate of the ambient temperature with a suitable standard uncertainty. Alternatively, known upper and lower limits for the temperature may be given using _diffrn_ambient_temperature_lt and *_gt. The same considerations hold true for ambient pressure.

The default for _diffrn_ambient_environment may be understood as `air', although formally it is impossible in the dictionary to specify a default for a free-text field.

The _diffrn_measured_fraction_theta_* items are provided in this category as an indication of the completeness of a set of reflection measurements. They are not as general as the other items in this category, as they apply only to monochromatic X-ray diffraction experiments, and they do not reflect the way macromolecular crystallographers tend to analyse the completeness of a data set as a function of resolution. When used, they must be accompanied by the value of the monochromatic radiation wavelength _diffrn_radiation_wavelength and relate to the maximum [\theta] angle for which the measured reflection count is considered as complete ( _diffrn_reflns_theta_full).

The other textual data items are provided for comment on other aspects of the handling of the crystal prior to the intensity measurement ( _diffrn_crystal_treatment), observations on the diffraction point symmetry, systematic absences and inferred space group or superspace group relationships ( _diffrn_symmetry_description) and any other comment on the intensity measurement process as a whole that cannot be accommodated elsewhere ( _diffrn_special_details).

3.2.2.2.2. Apparatus and instrumentation before the crystal

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The data items in these categories are as follows:

(a) DIFFRN_ATTENUATOR [Scheme scheme5]

(b) DIFFRN_RADIATION [Scheme scheme6]

(c) DIFFRN_RADIATION_WAVELENGTH [Scheme scheme7]

(d) DIFFRN_SOURCE [Scheme scheme8]

The bullet ([\bullet]) indicates a category key. The dagger ([\dagger]) indicates a deprecated item, which should not be used in the creation of new CIFs.

Attenuator properties are described by data items in the DIFFRN_ATTENUATOR category. Where an attenuator is used to reduce the intensity of an X-ray beam, this category may be used to describe the attenuator and its scaling factor. Details of multiple attenuator settings or materials can be included and each is identified by a code. A matching code value ( _diffrn_refln_attenuator_code) appears in the list of intensities against each reflection that must be scaled by the appropriate attenuation factor. In Example 3.2.2.1[link], the intensity of the second reflection has been reduced using a zirconium attenuator and must be multiplied by 16.976 to place it on the same scale as the first (and other unattenuated intensities).

Example 3.2.2.1. Attenuation of reflection intensities indicated by reference to attenuator scaling factors.

[Scheme scheme4]

The DIFFRN_RADIATION category describes the radiation used in the diffraction experiment and its experimental handling by collimation and monochromatization before it interacts with the sample. [Post-sample treatment of the radiation beam after diffraction (including passage through any analyser or collimator) is described by data items in the complementary DIFFRN_DETECTOR category.] Many of the data items in this category are descriptive. Additional information about the generation of the radiation is also found in the DIFFRN_SOURCE category.

The use of _diffrn_radiation_probe is strongly recommended as an unambiguous indicator of the probing radiation or particle type (its permitted values are x-ray, neutron, electron and gamma). The similar-sounding data name _diffrn_radiation_type allows for a more detailed description of the radiation type, such as white-beam or (using the CIF code for the Greek character α, \a) 'Cu K\a' for copper Kα radiation. In the case of monochromatic (or near-monochromatic) X-radiation, a better representation is given by the use of _diffrn_radiation_xray_symbol, which can have one of a limited number of values expressing the X-ray wavelength according to IUPAC conventions (e.g. K-L3, corresponding to the older Siegbahn notation Kα1). If this data item is used, the element used as the X-ray generator target must also be specified using the data item _diffrn_source_target. Software for reading CIFs should be aware of these two alternative representations.

If the radiation beam is monochromatic, the wavelength can be provided using _diffrn_radiation_wavelength. For a polychromatic beam, the other data items in the DIFFRN_RADIATION_WAVELENGTH category allow different wavelength components and an associated weighting factor for each component to be listed. In the list of experimental intensity measurements from a polychromatic beam (the DIFFRN_REFLN category, discussed below), each reflection has an associated _diffrn_refln_wavelength_id that must match the corresponding _diffrn_radiation_wavelength_id in this list.

The DIFFRN_SOURCE category specifies the characteristics of the radiation source in the experiment and is closely related to the DIFFRN_RADIATION category, which is concerned with the handling of the radiation beam before it reaches the specimen. (The now-deprecated data name _diffrn_radiation_source shows that there was no formal separation of the descriptions of the radiation generator and the radiation in the first release of the core dictionary.)

The general class of radiation is specified by the data name _diffrn_source, which is a free-text field. Typical entries would be 'sealed X-ray tube', 'nuclear reactor', 'synchrotron', 'spallation source', 'rotating-anode X-ray tube' or 'electron microscope'. It is clear that the category could describe non-X-ray experiments, but several of the data names within the category (e.g. _diffrn_source_target) have meanings that are specific to an X-ray experiment. New data names might be introduced if experiments using other radiation types become more common. For now, details that a user wishes to record that are not properly described by the existing data names may be stored in the _diffrn_source_details field.

3.2.2.2.3. Apparatus and instrumentation at the crystal

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The data items in these categories are as follows:

(a) DIFFRN_MEASUREMENT [Scheme scheme9]

(b) DIFFRN_ORIENT_MATRIX [Scheme scheme10]

(c) DIFFRN_ORIENT_REFLN [Scheme scheme11]

The bullet ([\bullet]) indicates a category key. Where multiple items within a category are marked with a bullet, they must be taken together to form a compound key.

The DIFFRN_MEASUREMENT category currently concerns specifically the mounting of the crystal and the details of the goniometer or other device on which it is mounted, with the exception of _diffrn_measurement_method, which is defined simply as the `method used to measure intensities'. In practice, for a typical single-crystal diffractometer setup this field is generally used to specify the scan type, as in Example 3.2.2.2[link], where the CIF code for the Greek character [\theta], \q, is used to indicate [\theta/2\theta] scans.

Example 3.2.2.2. An indication of the scan type of a diffractometer-based experiment.

[Scheme scheme12]

The orientation matrix gives the transformation between coordinates in a crystal-centric reference frame and those referred to the diffractometer axes. The data items defined in the DIFFRN_ORIENT_MATRIX category can be used to store the values in the matrix as recorded on an individual diffractometer and a reference to the convention used (in _diffrn_orient_matrix_type). However, the reference is not by itself sufficient to understand the transformation without additional external knowledge of the convention. Authors are encouraged to provide a full description of the convention in the text field _diffrn_orient_matrix_type.

The terminology UB refers to the conventional designation of the matrix relating reciprocal space and the reference frame of a diffractometer, calculated as the product of the orientation matrix U and the material matrix B by the method of Busing & Levy (1967[link]).

The reflections used to determine the orientation matrix can be listed in the category DIFFRN_ORIENT_REFLN. As discussed above, this list is useful for analysing the results on a diffractometer of known type, but is not useful if the convention for establishing the individual terms of the orientation matrix is not known.

3.2.2.2.4. Apparatus and instrumentation after the crystal

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The data items in this category are as follows:

DIFFRN_DETECTOR [Scheme scheme13]

The dagger ([\dagger]) indicates a deprecated item, which should not be used in the creation of new CIFs.

The DIFFRN_DETECTOR category is intended to describe the detector used to measure the scattered radiation, including any analyser and post-sample collimation. There are not many data names in this category, as it is not often necessary to know a lot about the detector beyond its make, model or name if it is made by a well known manufacturer. A record of the detector deadtime ( _diffrn_detector_dtime) and the resolution of an area detector ( _diffrn_detector_area_resol_mean) are useful details worth recording explicitly; other unusual or noteworthy details may be recorded in _diffrn_detector_details.

The deprecated items (retained for compatibility with the original release version) have been replaced by _diffrn_detector and _diffrn_detector_dtime to produce names better matched to the formal category assignment.

3.2.2.2.5. Intensity measurements

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The data items in these categories are as follows:

(a) DIFFRN_REFLN [Scheme scheme14]

(b) DIFFRN_REFLNS [Scheme scheme15]

(c) DIFFRN_REFLNS_CLASS [Scheme scheme16]

(d) DIFFRN_SCALE_GROUP [Scheme scheme17]

(e) DIFFRN_STANDARD_REFLN [Scheme scheme18]

(f) DIFFRN_STANDARDS [Scheme scheme19]

The bullet ([\bullet]) indicates a category key. Where multiple items within a category are marked with a bullet, they must be taken together to form a compound key. The arrow ([\rightarrow]) is a reference to a parent data item. The dagger ([\dagger]) indicates a deprecated item, which should not be used in the creation of new CIFs.

The DIFFRN_REFLN category describes the measured reflections in a diffraction experiment. Example 3.2.2.3[link] shows a listing from a CAD-4 single-crystal diffractometer.

Example 3.2.2.3. Listing of experimental diffraction intensities.

[Scheme scheme20]

Note that the data in this list refer to the raw measurements as acquired at the time of data collection. This is in contrast to the data in the REFLN list, which refer to the reflections after merging and scaling.

The meanings of most of the data names can be deduced by inspection of this example. Full definitions are given in the dictionary.

However, the category also contains a number of data items which are used to group blocks of reflections with additional properties described by data items in other categories. For example, a number of reflections in the list might share a common value of _diffrn_refln_scale_group_code; this value would link to a description in the DIFFRN_SCALE_GROUP category of the scaling factor that needs to be applied to this group of reflections to bring all intensities in the list on to a common scale. (For example, intensities might be obtained from individual films in a multi-film data set or from a number of separate crystals.)

Likewise, individual reflections might be marked to indicate that they were monitored as standards during the course of the experiment, using the data name _diffrn_refln_standard_code. These standard reflections may be listed separately in the DIFFRN_STANDARD_REFLN category, in which case they are labelled by _diffrn_standard_refln_code, which must have values matching those assigned in the main list of intensities.

Apart from these specific classes of reflections, the intensity data may be binned according to different criteria (e.g. for modulated structures the intensities are often partitioned into classes with the same value of [m=\textstyle\sum|m_i|], where the [m_i] are the integer coefficients indexing diffraction vectors in an n-dimensional representation). The data name _diffrn_refln_class_code is provided as a link to the different classes of reflections defined in the DIFFRN_REFLNS_CLASS category.

The DIFFRN_REFLNS category describes collective properties of the set of experimental intensity measurements and follows the convention (common elsewhere in the dictionary) of having a name very similar to the related DIFFRN_REFLN category, but using a plural form of the relevant term in the composite name. While the individual DIFFRN_REFLN entries appear in a looped list, the items in the DIFFRN_REFLNS category are not looped.

This category describes properties of the complete measurement set; descriptions of specific portions of the complete set are handled by the DIFFRN_REFLNS_CLASS category.

Several of the items that appear in this category can be derived from the contents of the DIFFRN_REFLN lists, but it is often convenient to list them separately for ease of access and as a consistency check.

Note the definition of _diffrn_reflns_number as the total number of measured intensities excluding those classed as `systematically absent' (reflections whose intensities are null as a consequence of crystallographic symmetry). There is no data item to specifically flag systematic absences (although one could assign a distinct _diffrn_refln_class_code value and define the relevant DIFFRN_REFLNS_CLASS). Because the measured diffraction data may (and often do) include reduced measurements and symmetry-equivalent reflection intensities, there is no formal way to check the value of _diffrn_reflns_number with dictionary-driven validation software. (Note that systematic absences are flagged in the structure-factor listing of the REFLN category.)

The data items in the DIFFRN_REFLNS_CLASS category record details about classes of reflections measured in the diffraction experiment. The user is free to assign classes according to arbitrary criteria; two specific cases, the marking of standard reflections and the clustering of intensities that need to be scaled by a common factor, have their own specific data items and associated categories, as discussed above. The example given in the dictionary (Example 3.2.2.4[link]) describes a one-dimensional incommensurately modulated structure, where each reflection class is defined by the number [m=\textstyle\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.

Example 3.2.2.4. Use of the DIFFRN_REFLNS_CLASS category to specify the main and satellite reflections collected for a modulated incommensurate structure.

[Scheme scheme21]

The DIFFRN_SCALE_GROUP category records scaling factors which must be applied to specific intensities in the DIFFRN_REFLN list to bring all the measurements on to a common scale (Example 3.2.2.5[link]). The scale factor _diffrn_scale_group_I_net is the factor by which the relevant net values in the intensities list must be multiplied. The intensities to which it must be applied are those in the intensities list marked with a _diffrn_refln_scale_group_code that matches the corresponding _diffrn_scale_group_code in this category.

Example 3.2.2.5. Scaling factors for reflections listed by group.

[Scheme scheme22]

The DIFFRN_STANDARD_REFLN category allows a separate tabulation of the reflections used as standards. Note that the actual measurements on these reflections are stored alongside all the other measurements in the DIFFRN_REFLN list. The results of the analysis of the standard reflections are described by the DIFFRN_STANDARDS category.

The DIFFRN_STANDARDS category describes the interval between measurements of the standard reflections and their overall intensity change (usually a decay, so that the relevant data name is _diffrn_standards_decay_%; this data item has a negative value if the final measured intensities are greater than the initial ones). The items assume a constant time interval (or number of counts) between the measurement of each standard and a single global value for the overall intensity change. If required, detailed tracking of the intensity change of individual standard reflections can be extracted from the DIFFRN_REFLN list provided the elapsed time at each measurement has been recorded ( _diffrn_refln_elapsed_time).

3.2.2.3. Experimental measurements on the crystal

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The categories describing experimental conditions are as follows:

EXPTL group
 EXPTL
 EXPTL_CRYSTAL
 EXPTL_CRYSTAL_FACE

The data items in these categories are as follows:

(a) EXPTL [Scheme scheme23]

(b) EXPTL_CRYSTAL [Scheme scheme24]

(c) EXPTL_CRYSTAL_FACE [Scheme scheme25]

The bullet ([\bullet]) indicates a category key. Where multiple items within a category are marked by a bullet, they must be taken together to form a compound key.

The EXPTL category is rather broadly named, but in practice is used to record details about any absorption correction applied and, using _exptl_special_details, any other details of the experimental work prior to intensity measurement not specifically described by other data items (e.g. _exptl_crystal_preparation).

The data items in the EXPTL_CRYSTAL category are designed to record details of experimental measurements on the crystal or crystals used. Since it is usually the case that just one crystal is used throughout the experiment, the category is presented as if it comprises non-looped data names. However, details of a number of crystals may be looped together, in which case _exptl_crystal_id is used to identify the different crystals and acts as the category key.

When different crystals are used to collect diffraction intensities, it is likely that the intensities collected from each crystal would need to be scaled by different factors, as recorded by the DIFFRN_SCALE_GROUP category and the _diffrn_refln_scale_group_code used for each individual reflection. In these circumstances, it would be good practice to use matching values of _diffrn_refln_scale_group_code and _exptl_crystal_id, although this is not mandatory.

Note that the F(000) value, which is often calculated as the integer number of electrons in the crystal unit cell, may contain dispersion contributions and is more properly calculated as[F(000) = \big[\big(\textstyle\sum f_r\big)^2 + \big(\sum f_i\big)^2\big]^{1/2},]where [f_r] and [f_i] are, respectively, the real and imaginary parts of the scattering factors at [\theta=0] and the sum is taken over each atom in the unit cell.

The crystal colour may be given as free text using the data item _exptl_crystal_colour. Alternatively, the standardized names developed by the International Centre for Diffraction Data to classify specimen colours may be constructed from the items _exptl_crystal_colour_lustre, *_modifier and *_primary, each of which has a restricted set of specific values.

The EXPTL_CRYSTAL_FACE category records details of the crystal faces. The faces are defined by Miller indices and their perpendicular distances from the centre of rotation of the crystal may be recorded in millimetres. Absolute orientations with respect to the goniometer angle settings may also be recorded. The category is currently constructed in a way that cannot distinguish between multiple crystals.

References

Busing, W. R. & Levy, H. A. (1967). Angle calculations for 3- and 4-circle X-ray and neutron diffractometers. Acta Cryst. 22, 457–464.








































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