Kathryn Shelley, former Department of Biochemistry Part II student and Garman group member, is the first author on a new paper published in Nature Communications. Her M.Biochemistry Part II project research has been published (Shelley and Garman - Quantifying and comparing radiation damage in the Protein Data Bank), as the culmination of her innovative and determined work both during and since graduating from Oxford. Kathryn's new metric will allow researchers to judge the degree of radiation damage inflicted on the protein during the X-ray diffraction experiment performed to determine the structure. Read on to find out more about Kathryn's work on radiation damage in protein crystallography.
Radiation damage remains one of the major bottlenecks to accurate structure solution in protein crystallography (PX). It can cause structural and chemical changes in protein crystals, and is hence an important consideration when assessing the quality and biological veracity of PX 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 PX 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 PX structures previously characterised as damaged, we calculate Bnet values for 93,978 PX PDB structures collected at cryo-temperatures. Our metric highlights a range of damage features many of which would remain unidentified by the other summary statistics typically calculated for PDB structures.
Figure: Observation of typical radiation damage features in structures with high Bnet values
Legend : wwPDB validation statistics, models and density maps for the 10 structures with the highest Bnet values in the PDB-REDO databank. For the eight structures with visible radiation damage artefacts in their associated electron density difference maps, a representative example is shown: for the two structures without such artefacts, the alternative causes of their high Bnet and Bnet-percentile values are shown instead. 2mF obs - DFcalc maps (blue) are contoured at 1.5 rmsd; Fobs - Fcalc difference density maps are contoured at +/- 3.0 rmsd (green/red).
Monday 14th March 2022