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![[Figure 6]](gm5124fig6mag.jpg)
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Figure 6
Metadata, models and density maps for representative examples of correctly classified cysteines, false positives and a false negative from the GAPDH dataset (PDB entries 1dbv, 5tso, 5j9g, 1ihy, 6gg7 and 3e5r) and validation dataset (PDB entries 1e3d, 8s6m, 5sb7 and 6jfq). PDB entry 6gg7 represents a true negative, where the cysteine is not predicted as oxidatively damaged despite the presence of clear reductive damage. For the false positives, PDB entries 3e5r, 1e3d, 8s6m and 5sb7, the reason for their flagging is depicted. PDB entry 6jfq represents a false negative where we were able to manually model a sulfinic acid into the electron density (purple) after deletion of the incorrectly placed water. There is no mention of radiation damage in structures which have a primary reference associated with them [PDB entries 1dbv (Didierjean et al., 1997  ), 1ihy (Shen et al., 2002), 6gg7 (McFarlane et al., 2019), 8s6m (Rosen et al., 2024), 1e3d (Matias et al., 2001) and 5sb7 (Mühlethaler et al., 2022)]. All of the crystals were produced in the presence of a reducing agent, with the exception of PDB entries 1e3d and 8s6m. Maps are contoured at 1.5 r.m.s.d. (2mFo − DFc, blue) and ±3.0 r.m.s.d. (Fo − DFc, green/red). |
![[Figure 6]](gm5124fig6.jpg)
 | STRUCTURAL BIOLOGY |
ISSN: 2059-7983
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