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| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102575 |
| This entry was created with PDB-REDO version 7.34. |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 112.854 Å | b: 52.919 Å | c: 44.942 Å | α: 90.00° | β: 103.14° | γ: 90.00° |
| Resolution | 1.75 Å | Reflections | 25961 | Test set | 1294 (5.0%) | ||
| R | 0.1880 | R-free | 0.2350 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.75 Å | Reflections | 25961 | Test set | 1294 (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 | 0.1970 | 0.2014 |
| R-free | 0.2400 | 0.2387 |
| Bond length RMS Z-score | 0.679 | 0.376 |
| Bond angle RMS Z-score | 1.025 | 0.653 |
| Model quality | ||
| Ramachandran plot normality | -1.782 34 | -1.342 44 |
| Rotamer normality | -1.547 67 | -0.455 86 |
| Coarse packing | -0.541 34 | -0.582 32 |
| Fine packing | -1.849 19 | -1.718 23 |
| Bump severity | 0.003 82 | 0.001 92 |
| Hydrogen bond satisfaction | 0.882 30 | 0.890 38 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 12 |
| Side chains flipped | 0 |
| Waters removed | 50 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |