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PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102868 |
This entry was created with PDB-REDO version 7.36. |
From original header | |||||||
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Spacegroup | C 1 2 1 | a: 112.250 Å | b: 52.872 Å | c: 44.476 Å | α: 90.00° | β: 103.02° | γ: 90.00° |
Resolution | 1.80 Å | Reflections | 23623 | Test set | 1181 (5.0%) | ||
R | 0.1860 | R-free | 0.2390 | ||||
According to PDB-REDO | |||||||
Resolution | 1.80 Å | Reflections | 23623 | Test set | 1181 (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 | 0.1993 | 0.2227 |
R-free | 0.2443 | 0.2734 |
Bond length RMS Z-score | 0.648 | 0.575 |
Bond angle RMS Z-score | 1.002 | 0.791 |
Model quality | ||
Ramachandran plot normality | -1.431 42 | -1.743 35 |
Rotamer normality | -1.271 72 | -1.596 66 |
Coarse packing | -0.277 47 | -0.322 45 |
Fine packing | -1.557 29 | -1.450 34 |
Bump severity | 0.008 64 | 0.009 61 |
Hydrogen bond satisfaction | 0.878 27 | 0.894 43 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 6 |
Side chains flipped | 0 |
Waters removed | 66 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 0 |
Residues fitting density worse | 0 |