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. 151-152

Section 3.6.5.3. Growth, description and analysis of the crystal

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

3.6.5.3. Growth, description and analysis of the crystal

| top | pdf |

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

EXPTL group
Crystal properties (§3.6.5.3.1[link])
 EXPTL
 EXPTL_CRYSTAL
 EXPTL_CRYSTAL_FACE
Crystal growth (§3.6.5.3.2[link])
 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

| top | pdf |

The data items in these categories are as follows:

(a) EXPTL [Scheme scheme31]

(b) EXPTL_CRYSTAL [Scheme scheme32]

(c) EXPTL_CRYSTAL_FACE [Scheme scheme33]

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.

Data items in these categories are used in the same way in the mmCIF and core CIF dictionaries, and Section 3.2.2.3[link] can be consulted for details (see Example 3.6.5.3[link]). 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

| top | pdf |

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[link] 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[link] 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.








































to end of page
to top of page