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![[Figure 2]](ai5006fig2mag.jpg)
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Figure 2
Errors in model building and refinement. (a) Shikonin in SARS-CoV-2 main protease (PDB entry 7ca8; Li et al., 2021  ). The B factors of the ligand are set uniformly to 20 Å2, whereas those of the surrounding residues are around 50 Å2. Difference map (green and red) contour level 0.248, r.m.s.d. 3.123 Å; 2mFo − DFc electron-density map (grey) contour level 0.306, r.m.s.d. 1.687 Å. (b) The re-refined model in (a) with proper ligand B factors. Difference map contour level 0.257, r.m.s.d. 3.509 Å, 2mFo − DFc electron-density map contour level 0.249, r.m.s.d. 3.409 Å. (c) Nonproline cis/twisted peptide bonds (red) located in SARS-CoV-2 helicase (PDB entry 6jyt; Jia et al., 2019). Map contour level 0.147, r.m.s.d. 1.104 Å. (d) Changing the cis-peptide bonds to a more plausible backbone conformation improves the density fit of (b). Map contour 0.117, r.m.s.d. 0.609 Å. (e) The blob associated with coordinated Zn2+ is assigned as a free Zn2+ ion, which is chemically not possible, and the deposited structure (PDB entry 6vyo; Center for Structural Genomics of Infectious Diseases, unpublished work) was later updated with a chloride ion next to the coordinated zinc ion instead. Map contour level 1.005, r.m.s.d. 2.711 Å. (f) A magnesium ion in SARS-CoV-2 endoRNase (PDB entry 6vww; Kim et al., 2020). The coordination geometry (tetrahedral) and bond valence (0.5) are indicated as outliers by CheckMyMetal (Zheng et al., 2017); they are expected to be octahedral and 2.0, respectively. A water molecule would be more plausible. Map contour level 0.569, r.m.s.d. 2.620 Å; difference density at contour level 0.108, r.m.s.d. 3.000 Å. |
![[Figure 2]](ai5006fig2.jpg)
 | STRUCTURAL BIOLOGY |
ISSN: 2059-7983
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