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![[Figure 5]](qq5002fig5mag.jpg)
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Figure 5
Identifying specific radiation damage with the BDamage, Bnet and Bnet-percentile metrics in cryo-temperature protein crystal structures. (a) The BDamage metric identifies atoms with high B-factor values relative to other atoms in a similar local packing-density environment in the crystal. (i) Definition of the BDamage metric. (ii) Box plots of the isotropic atomic B-factor and BDamage values for glutamate side-chain O atoms in low-dose and high-dose data sets collected from lysozyme and ribonuclease A (PDB entries 2blx, 2bly, 2blp and 2blz; Nanao et al., 2005  ). Boxes represent the median and interquartile range (IQR), outliers are represented as black dots, and whiskers represent the range (excluding any outliers). This figure was adapted from Gerstel et al. (2015). (b) The Bnet metric identifies structures whose aspartate and glutamate side-chain O atoms have high BDamage values in comparison to the rest of the structure. Bnet is calculated by plotting a kernel density estimate (KDE) plot of the BDamage values of aspartate and glutamate side-chain O atoms. The area under the curve is calculated to the left (A) and right (B) of the median BDamage value of all atoms in the structure; Bnet is then calculated by dividing B by A. (i) Definition of the Bnet metric; KDE plots demonstrating the Bnet calculation are shown for (ii) a low-dose structure and (iii) a high-dose structure (PDB entries 5mcc and 5mcn, respectively; Bury et al., 2017). (iv) Bnet is correlated with dose. The plot shows Bnet values calculated for nine radiation-damage series (PDB codes and references are provided in Shelley & Garman, 2022). These figures were adapted from Shelley & Garman (2022). (c) wwPDB validation statistics, models and density maps for two of the most damaged cryo-temperature protein crystal structures deposited in the PDB, as determined using the Bnet and Bnet-percentile metrics. 2mFobs − DFcalc maps (blue) are contoured at 1.5 r.m.s.d.; Fobs − Fcalc difference density maps are contoured at ±3.0 r.m.s.d., with positive and negative density coloured green and red, respectively. This figure was adapted from Shelley & Garman (2022). |
![[Figure 5]](qq5002fig5.jpg)
 | STRUCTURAL BIOLOGY |
ISSN: 2059-7983
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