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PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102277 |
This entry was created with PDB-REDO version 7.36. |
From original header | |||||||
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Spacegroup | C 1 2 1 | a: 112.297 Å | b: 52.885 Å | c: 44.537 Å | α: 90.00° | β: 103.11° | γ: 90.00° |
Resolution | 1.58 Å | Reflections | 33814 | Test set | 1673 (4.9%) | ||
R | 0.1890 | R-free | 0.2370 | ||||
According to PDB-REDO | |||||||
Resolution | 1.58 Å | Reflections | 33814 | Test set | 1673 (4.9%) | 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 | 0.2070 | 0.2004 |
R-free | 0.2485 | 0.2493 |
Bond length RMS Z-score | 0.656 | 0.359 |
Bond angle RMS Z-score | 1.021 | 0.647 |
Model quality | ||
Ramachandran plot normality | -1.586 38 | -1.629 37 |
Rotamer normality | -1.206 74 | -0.168 90 |
Coarse packing | -0.402 41 | -0.440 39 |
Fine packing | -1.633 26 | -1.575 28 |
Bump severity | 0.009 61 | 0.003 82 |
Hydrogen bond satisfaction | 0.847 13 | 0.861 17 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 7 |
Side chains flipped | 0 |
Waters removed | 36 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 3 |
Residues fitting density worse | 0 |