Quantifying and comparing radiation damage in the Protein Data Bank

Journal article

AbstractRadiation 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.

Authors: Shelley, KL; Garman, EF

• Publication status: Published
• Peer review status: Peer reviewed
• Publisher: Nature Research
• Journal: Nature Communications
• Volume: 13
• Issue: 1
• Pages: 1314-1314
• Article number: 1314
• Publication date: 2022-03-14
• DOI: 10.1038/s41467-022-28934-0
• EISSN: 2041-1723
• ISSN: 2041-1723
• Language: English
• Keywords: Computational biology; Optics; Chemistry; Radiation; Protein Data Bank; Crystal structure; Crystallography; Computer science; Protein Data Bank (RCSB PDB); Physics; Radiation damage; Engineering; Metric (unit); Protein structure; Biology; Biological system; Data mining; Materials science; Biochemistry; Protein crystallization