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. 3.6, pp. 148-149

Section 3.6.5.1. Crystal cell parameters and measurement conditions

P. M. D. Fitzgerald,a* J. D. Westbrook,b P. E. Bourne,c B. McMahon,d K. D. Watenpaughe and H. M. Bermanf

aMerck 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

3.6.5.1. 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
 CELL_MEASUREMENT_REFLN

The mmCIF dictionary differs from the core CIF dictionary in assigning separate categories to data names that define the crystal unit-cell parameters and to data names relating to the experimental determination of the unit cell. Details of the unit-cell parameters are given in the CELL category and data items in the distinct CELL_MEASUREMENT category are used to describe how the unit-cell parameters were measured. The category CELL_MEASUREMENT_REFLN, which is used to list the reflections used in the unit-cell determination, is common to the core and mmCIF dictionaries.

The data items in these categories are as follows:

(a) CELL [Scheme scheme11]

(b) CELL_MEASUREMENT [Scheme scheme12]

(c) CELL_MEASUREMENT_REFLN [Scheme scheme13]

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. 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.

The summary above includes the formal category keys that have been introduced in mmCIF because the corresponding core categories do not expect looped data, and therefore do not require the specification of a unique identifier. In the relational model of DDL2, all categories are considered to be tables and therefore each category must have a unique identifier. Where core CIF categories have one or more data names that fulfil the role of table-row identifiers, these have generally been carried over as category keys in the mmCIF dictionary (for example, the data items that correspond to the h, k and l Miller indices of a reflection in the CELL_MEASUREMENT_REFLN category).

Example 3.6.5.1[link] shows how data items from these categories are used in practice and shows the use of separate data items to record standard uncertainties of measurable quantities.

Example 3.6.5.1. Cell constants and their measurement for an HIV-1 protease crystal (PDB 5HVP) described with data items in the CELL and CELL_MEASUREMENT categories (Fitzgerald et al., 1990[link]).

[Scheme scheme14]

References

Fitzgerald, P. M. D., McKeever, B. M., VanMiddlesworth, J. F., Springer, J. P., Heimbach, J. C., Leu, C.-T., Kerber, W. K., Dixon, R. A. F. & Darke, P. L. (1990). Crystallographic analysis of a complex between human immunodeficiency virus type 1 protease and acetyl-pepstatin at 2.0-A resolution. J. Biol. Chem. 265, 14209–14219.








































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