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PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102306 |
This entry was created with PDB-REDO version 7.34 using the deposited PDB model |
From original header | |||||||
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Spacegroup | C 1 2 1 | a: 112.254 Å | b: 52.664 Å | c: 44.535 Å | α: 90.00° | β: 103.02° | γ: 90.00° |
Resolution | 1.48 Å | Reflections | 40622 | Test set | 1979 (4.9%) | ||
R | 0.1870 | R-free | 0.2240 | ||||
According to PDB-REDO | |||||||
Resolution | 1.48 Å | Reflections | 40622 | Test set | 1979 (4.9%) | ||
Twin | false | Radiation damage | N/A | ||||
PDB-REDO files | |||||||
Re-refined and rebuilt structure | Re-refined (only) structure |
All files
(compressed) |
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Links | |||||||
PDBe | RCSB PDB | 3D bionotes | Proteopedia |
Original | PDB-REDO | |
---|---|---|
Crystallographic refinement | ||
R | 0.1950 | 0.1970 |
R-free | 0.2298 | 0.2273 |
Bond length RMS Z-score | 0.659 | 0.377 |
Bond angle RMS Z-score | 1.020 | 0.667 |
Model quality | ||
Ramachandran plot normality | -1.083 51 | -0.977 54 |
Rotamer normality | -0.636 83 | 0.085 93 |
Coarse packing | -0.251 49 | -0.245 49 |
Fine packing | -1.636 26 | -1.372 37 |
Bump severity | 0.003 82 | 0.004 78 |
Hydrogen bond satisfaction | 0.884 32 | 0.883 31 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 8 |
Side chains flipped | 0 |
Waters removed | 41 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 0 |
Residues fitting density worse | 0 |