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RABDAM : quantifying specific radiation damage in individual protein crystal structures
Author(s) -
Shelley Kathryn L.,
Dixon Thomas P. E.,
Brooks-Bartlett Jonathan C.,
Garman Elspeth F.
Publication year - 2018
Publication title -
journal of applied crystallography
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.429
H-Index - 162
ISSN - 1600-5767
DOI - 10.1107/s1600576718002509
Subject(s) - radiation damage , protein data bank (rcsb pdb) , metric (unit) , protein data bank , synchrotron radiation , protein crystallization , reflection (computer programming) , crystallography , computer science , materials science , radiation , physics , biological system , chemistry , protein structure , biology , optics , nuclear magnetic resonance , engineering , crystallization , operations management , thermodynamics , programming language
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.