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| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102432 |
| This entry was created with PDB-REDO version 7.34. |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 112.771 Å | b: 52.953 Å | c: 44.472 Å | α: 90.00° | β: 103.09° | γ: 90.00° |
| Resolution | 1.58 Å | Reflections | 32953 | Test set | 1628 (4.9%) | ||
| R | 0.1950 | R-free | 0.2370 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.58 Å | Reflections | 32953 | Test set | 1628 (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 | 0.2046 | 0.2052 |
| R-free | 0.2447 | 0.2458 |
| Bond length RMS Z-score | 0.644 | 0.404 |
| Bond angle RMS Z-score | 1.015 | 0.680 |
| Model quality | ||
| Ramachandran plot normality | -1.540 39 | -1.550 39 |
| Rotamer normality | -1.272 72 | -0.426 87 |
| Coarse packing | -0.318 45 | -0.375 42 |
| Fine packing | -1.627 26 | -1.508 31 |
| Bump severity | 0.004 78 | 0.003 82 |
| Hydrogen bond satisfaction | 0.898 48 | 0.883 31 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 9 |
| Side chains flipped | 0 |
| Waters removed | 49 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |