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.
Shelley, K. L., Dixon, T. P. E., Brooks-Bartlett, J. C., & Garman, E. F. (2018). RABDAM : quantifying specific radiation damage in individual protein crystal structures . Journal of Applied Crystallography, 51(2), 552–559. https://doi.org/10.1107/s1600576718002509