Data collection

Fitzgerald, P. M. D.; Westbrook, J. D.; Bourne, P. E.; McMahon, B.; Watenpaugh, K. D.; Berman, H. M.

doi:10.1107/97809553602060000738

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

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International Tables for Crystallography (2006). Vol. G. ch. 3.6, pp. 149-151

Section 3.6.5.2. Data collection

P. M. D. Fitzgerald,^a ^* J. D. Westbrook,^b P. E. Bourne,^c B. McMahon,^d K. D. Watenpaugh^e and H. M. Berman^f

^a Merck Research Laboratories, Rahway, New Jersey, USA,^bProtein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, Department of Chemistry and Chemical Biology, 610 Taylor Road, Piscataway, New Jersey, USA,^cResearch Collaboratory for Structural Bioinformatics, San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0537, USA,^dInternational Union of Crystallography, 5 Abbey Square, Chester CH1 2HU, England,^eretired; formerly Structural, Analytical and Medicinal Chemistry, Pharmacia Corporation, Kalamazoo, Michigan, USA, and ^fProtein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, Department of Chemistry and Chemical Biology, 610 Taylor Road, Piscataway, New Jersey, USA
Correspondence e-mail: paula_fitzgerald@merck.com

3.6.5.2. Data collection

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The categories describing data collection are as follows:

DIFFRN group

DIFFRN

DIFFRN_ATTENUATOR

DIFFRN_DETECTOR

DIFFRN_MEASUREMENT

DIFFRN_ORIENT_MATRIX

DIFFRN_ORIENT_REFLN

DIFFRN_RADIATION

DIFFRN_RADIATION_WAVELENGTH

DIFFRN_REFLN

DIFFRN_REFLNS

DIFFRN_REFLNS_CLASS

DIFFRN_SCALE

DIFFRN_SOURCE

DIFFRN_STANDARD_REFLN

DIFFRN_STANDARDS

The categories in the DIFFRN category group describe the diffraction experiment. Data items in the DIFFRN category itself can be used to give overall information about the experiment, such as the temperature and pressure. Examples of the other categories are DIFFRN_DETECTOR, which is used for describing the detector used for data collection, and DIFFRN_SOURCE, which is used to give details of the source of the radiation used in the experiment. Data items in the DIFFRN_REFLN category can be used to give information about the raw data and data items in the DIFFRN_REFLNS category can be used to give information about all the reflection data collectively.

The data items in the categories in the DIFFRN group are as follows:

(a) DIFFRN [Scheme scheme15]

(b) DIFFRN_ATTENUATOR [Scheme scheme16]

(d) DIFFRN_MEASUREMENT [Scheme scheme18]

(e) DIFFRN_ORIENT_MATRIX [Scheme scheme19]

(f) DIFFRN_ORIENT_REFLN [Scheme scheme20]

(g) DIFFRN_RADIATION [Scheme scheme21]

(h) DIFFRN_RADIATION_WAVELENGTH [Scheme scheme22]

(i) DIFFRN_REFLN [Scheme scheme23]

(j) DIFFRN_REFLNS [Scheme scheme24]

(k) DIFFRN_REFLNS_CLASS [Scheme scheme25]

(l) DIFFRN_SCALE_GROUP [Scheme scheme26]

(m) DIFFRN_SOURCE [Scheme scheme27]

(n) DIFFRN_STANDARD_REFLN [Scheme scheme28]

(o) DIFFRN_STANDARDS [Scheme scheme29]

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. Items in italics have aliases in the core CIF dictionary formed by changing the full stop (.) to an underscore (_) except where indicated by the $[\sim]$ symbol. Data items marked with a plus (+) have companion data names for the standard uncertainty in the reported value, formed by appending the string _esd to the data name listed.

To a very great extent, data items in the DIFFRN category group are used in the same way in the mmCIF and core CIF dictionaries, and Section 3.2.2.2 can be consulted for details. Example 3.6.5.2 shows how these categories are used to describe the data collection for a macromolecule.

Example 3.6.5.2. Data collection for an HIV-1 protease crystal (PDB 5HVP) described with data items in the DIFFRN and related categories.

[Scheme scheme30]

There is, however, one important difference. An mmCIF may describe several separate diffraction experiments that were conducted with a common purpose; each such experiment would be given a unique value of _diffrn.id, the key for the DIFFRN category. Descriptions of features of that experiment in related categories would be given a matching identifier with the same value (e.g. _diffrn_detector.diffrn_id). The use of the suffix *.diffrn_id for the key data names in each related category emphasizes the connection to the parent experiment.

As a consequence, there are differences between the mmCIF and core CIF dictionaries in the definition of the category keys for the DIFFRN categories. These differences were introduced in order to accommodate data from more than one experiment in the same table. For example, in the core CIF dictionary, the Miller indices _diffrn_refln_index_h, *_k and *_l play the role of the category key for the DIFFRN_REFLN category. In the mmCIF dictionary, the category key is formed by the data items _diffrn_refln.id and _diffrn_refln.diffrn_id.

References

International Tables for Crystallography (2006). Vol. G. ch. 3.6, pp. 149-151