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Quantifying and comparing radiation damage in the Protein Data Bank.

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 B_net metric. B_net 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 B_net successfully detects damage in 23 different crystal structures previously characterised as damaged, we calculate B_net 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.

SUBMITTER: Shelley KL

PROVIDER: S-EPMC8921271 | biostudies-literature | 2022 Mar

REPOSITORIES: biostudies-literature

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Quantifying and comparing radiation damage in the Protein Data Bank.

Shelley Kathryn L KL Garman Elspeth F EF

Nature communications 20220314 1

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 B<sub>net</sub> metric. B< ...[more]

PMID: 35288575

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