Quantifying and comparing radiation damage in the Protein Data Bank

Kathryn L. Shelley,Elspeth F. Garman

doi:10.1038/s41467-022-28934-0

Kathryn L. Shelley, Elspeth F. Garman

Open Access

https://doi.org/10.1038/s41467-022-28934-0

Copy DOI

Journal: Nature Communications	Publication Date: Mar 14, 2022
Citations: 20	License type: open-access

Affiliation: University of Oxford, University of Bristol

Abstract

Radiation damage remains one of the major bottlenecks to accurate structure solution in protein crystallography. It can induce structural and chemical changes in protein crystals, and is hence an important consideration when assessing the quality and biological veracity of crystal structures in repositories like the Protein Data Bank (PDB). However, detection of radiation damage artefacts has traditionally proved very challenging. To address this, here we introduce the Bnet metric. Bnet summarises in a single value the extent of damage suffered by a crystal structure by comparing the B-factor values of damage-prone and non-damage-prone atoms in a similar local environment. After validating that Bnet successfully detects damage in 23 different crystal structures previously characterised as damaged, we calculate Bnet values for 93,978 PDB crystal structures. Our metric highlights a range of damage features, many of which would remain unidentified by the other summary statistics typically calculated for PDB structures.

Highlights

Radiation damage remains one of the major bottlenecks to accurate structure solution in protein crystallography
When a structure suffers specific radiation damage, the B-factor values of the affected atoms increase relative to unaffected atoms
Here we have developed the Bnet-percentile values (Bnet) metric, which assesses the extent of radiation damage suffered by cryo-temperature (80–120 K) PX structures

Summary

Introduction

Radiation damage remains one of the major bottlenecks to accurate structure solution in protein crystallography. Despite the development of various damage mitigation strategies, including cryo-cooling[1] and optimisation of the data collection strategy using software such as BEST2 or RADDOSE-3D3, data collection methodologies using the increasing flux densities of synchrotron light sources have resulted in radiation damage remaining one of the major challenges in protein crystallography. This problem will only be further exacerbated as the recently constructed fourthgeneration synchrotron sources come online. Specific radiation damage is usually studied by identifying differences between successive datasets collected from the same crystal(s)

Methods

Results

Conclusion