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PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102327 |
This entry was created with PDB-REDO version 7.36. |
From original header | |||||||
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Spacegroup | C 1 2 1 | a: 112.504 Å | b: 52.706 Å | c: 44.481 Å | α: 90.00° | β: 102.91° | γ: 90.00° |
Resolution | 1.74 Å | Reflections | 25996 | Test set | 1291 (5.0%) | ||
R | 0.1830 | R-free | 0.2300 | ||||
According to PDB-REDO | |||||||
Resolution | 1.74 Å | Reflections | 25996 | Test set | 1291 (5.0%) | ||
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 | 0.1885 | 0.1927 |
R-free | 0.2331 | 0.2286 |
Bond length RMS Z-score | 0.660 | 0.367 |
Bond angle RMS Z-score | 1.005 | 0.647 |
Model quality | ||
Ramachandran plot normality | -1.705 35 | -1.211 47 |
Rotamer normality | -0.902 79 | -0.082 91 |
Coarse packing | -0.266 48 | -0.264 48 |
Fine packing | -1.435 34 | -1.396 36 |
Bump severity | 0.007 67 | 0.010 58 |
Hydrogen bond satisfaction | 0.895 44 | 0.889 37 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 13 |
Side chains flipped | 0 |
Waters removed | 41 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 0 |
Residues fitting density worse | 1 |