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![[Figure 4]](qq5002fig4mag.jpg)
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Figure 4
Identifying damage in Fobs(late) − Fobs(early) difference maps with RIDL. (a) RIDL calculates difference maps and divides them into voxels. The program measures the damage to atom j by first identifying the voxels within a radius rj of atom j and then calculating the Dneg metric (as well as several other metrics). ρΔ(v) and ρcalc(v) are the density values at voxel v in an Fobs(late) − Fobs(early) map and a map calculated directly from Fcalc, respectively, whilst ![[V_{\rm atom}^-]](teximages/qq5002fi1.svg){kind=small} refers to all of the voxels with negative difference density in the Fobs(late) − Fobs(early) map within a radius rj of atom j. This figure was adapted from Bury et al. (2018 ). (b) Difference density maps produced by RIDL for a low-dose and a high-dose data set collected from a xylose isomerase crystal (PDB entry 6qrr; Taberman et al., 2019); positive/negative difference density (contoured at ±3σ) is coloured green/red and shown separately in the top/bottom images for clarity. The xylose isomerase active site is shown, demonstrating the accrual of radiation damage in the higher relative to the lower dose data set. This figure was adapted from Taberman et al. (2019). (c) Difference density maps produced by RIDL for four data sets of increasing dose collected from a crystal of a DNA 16-mer (PDB entry 6qt1; Bugris et al., 2019). Maps are contoured at ±3σ, with positive/negative density coloured green/red. Arrows indicate examples of sites where damage accumulates with increasing dose; damage artefacts are predominantly localized around the sugar-phosphate backbone. This figure was adapted from Bugris et al. (2019). All data leading to the structures presented in (b) and (c) were collected at 100 K. |
![[Figure 4]](qq5002fig4.jpg)
 | STRUCTURAL BIOLOGY |
ISSN: 2059-7983
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