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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 BDamage metric has helped to address this problem. BDamage 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 BDamage 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.

Original publication

DOI

10.1107/S1600576718002509

Type

Journal article

Journal

J Appl Crystallogr

Publication Date

01/04/2018

Volume

51

Pages

552 - 559

Keywords

BDamage, PDB, Protein Data Bank, RABDAM, atomic B factors, atomic displacement parameters, computer programs, protein crystallography, radiation damage