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| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z31432226 |
| This entry was created with PDB-REDO version 7.34. |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 111.604 Å | b: 52.401 Å | c: 44.322 Å | α: 90.00° | β: 102.78° | γ: 90.00° |
| Resolution | 1.63 Å | Reflections | 30744 | Test set | 1513 (4.9%) | ||
| R | 0.1850 | R-free | 0.2280 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.63 Å | Reflections | 30744 | Test set | 1513 (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 | 0.2602 | 0.2461 |
| R-free | 0.2883 | 0.2789 |
| Bond length RMS Z-score | 0.653 | 0.569 |
| Bond angle RMS Z-score | 0.999 | 0.798 |
| Model quality | ||
| Ramachandran plot normality | -1.922 31 | -1.959 30 |
| Rotamer normality | -0.814 81 | -1.217 73 |
| Coarse packing | -0.226 50 | -0.234 50 |
| Fine packing | -1.518 31 | -1.211 44 |
| Bump severity | 0.003 82 | 0.014 49 |
| Hydrogen bond satisfaction | 0.804 5 | 0.807 6 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 6 |
| Side chains flipped | 0 |
| Waters removed | 141 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 4 |
| Residues fitting density worse | 0 |