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PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102575 |
This entry was created with PDB-REDO version 7.34. |
From original header | |||||||
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Spacegroup | C 1 2 1 | a: 112.854 Å | b: 52.919 Å | c: 44.942 Å | α: 90.00° | β: 103.14° | γ: 90.00° |
Resolution | 1.75 Å | Reflections | 25961 | Test set | 1294 (5.0%) | ||
R | 0.1880 | R-free | 0.2350 | ||||
According to PDB-REDO | |||||||
Resolution | 1.75 Å | Reflections | 25961 | Test set | 1294 (5.0%) | Twin | false |
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 | 0.1970 | 0.2014 |
R-free | 0.2400 | 0.2387 |
Bond length RMS Z-score | 0.679 | 0.376 |
Bond angle RMS Z-score | 1.025 | 0.653 |
Model quality | ||
Ramachandran plot normality | -1.782 34 | -1.342 44 |
Rotamer normality | -1.547 67 | -0.455 86 |
Coarse packing | -0.541 34 | -0.582 32 |
Fine packing | -1.849 19 | -1.718 23 |
Bump severity | 0.003 82 | 0.001 92 |
Hydrogen bond satisfaction | 0.882 30 | 0.890 38 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 12 |
Side chains flipped | 0 |
Waters removed | 50 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 0 |
Residues fitting density worse | 0 |