Experimental measurements

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. 148-152

Section 3.6.5. Experimental measurements

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. Experimental measurements

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The CELL, DIFFRN and EXPTL category groups are used to describe the crystallographic experiment. The data items used for this purpose in mmCIF are for the most part identical to those in the core CIF dictionary. A complete discussion of the data names in each category may be found in Section 3.2.2 .

mmCIF also contains the new categories EXPTL_CRYSTAL_GROW and EXPTL_CRYSTAL_GROW_COMP (Section 3.6.5.3.2), which are used to provide a more structured description of crystallization than is available in the core CIF dictionary.

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]

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 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).

[Scheme scheme14]

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.

3.6.5.3. Growth, description and analysis of the crystal

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The categories describing the crystal properties and growth are as follows:

EXPTL group

Crystal properties (§3.6.5.3.1

)

EXPTL

EXPTL_CRYSTAL

EXPTL_CRYSTAL_FACE

Crystal growth (§3.6.5.3.2

)

EXPTL_CRYSTAL_GROW

EXPTL_CRYSTAL_GROW_COMP

Categories in the EXPTL category group are used to describe experimental measurements on the crystal (e.g. of its shape, size and density) and the growth of the crystal. Data items in the EXPTL category are used to describe the gross properties of the crystal or crystals used in the experiment. Data items in the EXPTL_CRYSTAL category are used to describe the crystal properties in detail and allow for cases where multiple crystals are used. The data items in the EXPTL_CRYSTAL_FACE category are used to describe the crystal faces.

Data items for describing crystal growth are given in two categories that are not found in the current version of the core CIF dictionary. Data items in the EXPTL_CRYSTAL_GROW category are used to describe the conditions and methods used to grow the crystals, and data items in the EXPTL_CRYSTAL_GROW_COMP category can be used to list the components of the solutions in which the crystals were grown.

3.6.5.3.1. Crystal properties

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The data items in these categories are as follows:

(a) EXPTL [Scheme scheme31]

(b) EXPTL_CRYSTAL [Scheme scheme32]

Data items in these categories are used in the same way in the mmCIF and core CIF dictionaries, and Section 3.2.2.3 can be consulted for details (see Example 3.6.5.3). Identifiers have been introduced to the categories to provide the formal category keys required by the DDL2 data model.

Example 3.6.5.3. The crystal used in the determination of an HIV-1 protease structure (PDB 5HVP) described using data items in the EXPTL and EXPTL_CRYSTAL categories.

[Scheme scheme34]

3.6.5.3.2. Crystal growth

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The data items in these categories are as follows:

(a) EXPTL_CRYSTAL_GROW [Scheme scheme35]

(b) EXPTL_CRYSTAL_GROW_COMP [Scheme scheme36]

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. 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.

Crystallization strategies and protocols are very varied and may not lend themselves to a formal tabulation. Common or well defined techniques may be indicated using the data item _exptl_crystal_grow.method, and a literature reference, where appropriate, may be given using _exptl_crystal_grow.method_ref. Frequently, however, a detailed description of methodology is required; this can be given in _exptl_crystal_grow.details. Example 3.6.5.4 shows how information about strategies that were attempted and proved unsuccessful can be recorded. In circumstances such as this, the data item _exptl_crystal_grow.pH would record the final pH.

Example 3.6.5.4. The growth of HIV-1 protease crystals (PDB 5HVP) described with data items in the EXPTL_CRYST_GROW and EXPTL_CRYSTAL_GROW_COMP categories.

[Scheme scheme37]

Where the crystallization protocol is well defined, it is useful to list the individual components of the solution in the category EXPTL_CRYSTAL_GROW_COMP. Example 3.6.5.4 labels the solutions used as 1 and 2, in accordance with the convention that solution 1 contains the molecule to be crystallized and solution 2 (and if necessary additional solutions) contains the precipitant. However, it is permissible and may be preferable to use more explicit labels such as `well solution' in the _exptl_crystal_grow_comp.sol_id field.

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.Google Scholar

International Tables for Crystallography (2006). Vol. G. ch. 3.6, pp. 148-152