期刊
JOURNAL OF APPLIED CRYSTALLOGRAPHY
卷 51, 期 -, 页码 552-559出版社
INT UNION CRYSTALLOGRAPHY
DOI: 10.1107/S1600576718002509
关键词
radiation damage; atomic B factors; atomic displacement parameters; B-Damage; RABDAM; Protein Data Bank; PDB; protein crystallography; computer programs
资金
- BBSRC (Biotechnology and Biological Sciences Research Council)
- Moritz-Heyman Scholarship Programme
Radiation damage remains one of the major limitations to accurate structure determination in protein crystallography (PX). Despite the use of cryo-cooling techniques, it is highly probable that a number of the structures deposited in the Protein Data Bank (PDB) have suffered substantial radiation damage as a result of the high flux densities of third generation synchrotron X-ray sources. Whereas the effects of global damage upon diffraction pattern reflection intensities are readily detectable, traditionally the (earlier onset) site-specific structural changes induced by radiation damage have proven difficult to identify within individual PX structures. More recently, however, development of the B-Damage metric has helped to address this problem. B-Damage is a quantitative, per-atom metric identifies potential sites of specific damage by comparing the atomic B-factor values of atoms that occupy a similar local packing density environment in the structure. Building upon this past work, this article presents a program, RABDAM, to calculate the B-Damage metric for all selected atoms within any standard-format PDB or mmCIF file. RABDAM provides several useful outputs to assess the extent of damage suffered by an input PX structure. This free and open-source software will allow assessment and improvement of the quality of PX structures both previously and newly deposited in the PDB.
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