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| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102704 |
| This entry was created with PDB-REDO version 7.36. |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 112.943 Å | b: 52.908 Å | c: 44.529 Å | α: 90.00° | β: 103.09° | γ: 90.00° |
| Resolution | 1.78 Å | Reflections | 24602 | Test set | 1226 (5.0%) | ||
| R | 0.1920 | R-free | 0.2470 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.78 Å | Reflections | 24602 | Test set | 1226 (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 | 0.2097 | 0.2193 |
| R-free | 0.2598 | 0.2600 |
| Bond length RMS Z-score | 0.658 | 0.370 |
| Bond angle RMS Z-score | 1.014 | 0.655 |
| Model quality | ||
| Ramachandran plot normality | -2.038 29 | -1.623 37 |
| Rotamer normality | -1.373 70 | -0.598 84 |
| Coarse packing | -0.333 44 | -0.352 44 |
| Fine packing | -1.593 28 | -1.404 36 |
| Bump severity | 0.009 61 | 0.009 61 |
| Hydrogen bond satisfaction | 0.885 33 | 0.869 21 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 8 |
| Side chains flipped | 0 |
| Waters removed | 39 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |