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| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z2856434899 |
| This entry was created with PDB-REDO version 7.34. |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 113.212 Å | b: 53.034 Å | c: 44.302 Å | α: 90.00° | β: 102.95° | γ: 90.00° |
| Resolution | 1.68 Å | Reflections | 29081 | Test set | 1434 (4.9%) | ||
| R | 0.1760 | R-free | 0.2240 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.68 Å | Reflections | 29081 | Test set | 1434 (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 | 0.1838 | 0.1886 |
| R-free | 0.2285 | 0.2263 |
| Bond length RMS Z-score | 0.668 | 0.504 |
| Bond angle RMS Z-score | 1.032 | 0.749 |
| Model quality | ||
| Ramachandran plot normality | -1.370 43 | -1.062 51 |
| Rotamer normality | -1.200 74 | -0.609 84 |
| Coarse packing | -0.298 46 | -0.305 46 |
| Fine packing | -1.478 33 | -1.245 43 |
| Bump severity | 0.008 64 | 0.005 74 |
| Hydrogen bond satisfaction | 0.874 24 | 0.894 43 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 7 |
| Side chains flipped | 0 |
| Waters removed | 77 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 2 |
| Residues fitting density worse | 0 |