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PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102425 |
This entry was created with PDB-REDO version 7.34. |
From original header | |||||||
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Spacegroup | C 1 2 1 | a: 113.544 Å | b: 52.903 Å | c: 44.618 Å | α: 90.00° | β: 103.16° | γ: 90.00° |
Resolution | 2.15 Å | Reflections | 14085 | Test set | 725 (5.1%) | ||
R | 0.1740 | R-free | 0.2780 | ||||
According to PDB-REDO | |||||||
Resolution | 2.15 Å | Reflections | 14085 | Test set | 725 (5.1%) | 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 | 0.1875 | 0.2069 |
R-free | 0.2866 | 0.2849 |
Bond length RMS Z-score | 0.698 | 0.362 |
Bond angle RMS Z-score | 1.047 | 0.627 |
Model quality | ||
Ramachandran plot normality | -3.011 16 | -1.940 31 |
Rotamer normality | -2.640 46 | -0.957 78 |
Coarse packing | -0.582 32 | -0.589 32 |
Fine packing | -1.785 21 | -1.576 28 |
Bump severity | 0.006 70 | 0.003 82 |
Hydrogen bond satisfaction | 0.877 26 | 0.870 22 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 10 |
Side chains flipped | 0 |
Waters removed | 76 |
Peptides flipped | 1 |
Chiralities fixed | 0 |
Residues fitting density better | 2 |
Residues fitting density worse | 0 |