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| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102425 |
| This entry was created with PDB-REDO version 7.34. |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 113.544 Å | b: 52.903 Å | c: 44.618 Å | α: 90.00° | β: 103.16° | γ: 90.00° |
| Resolution | 2.15 Å | Reflections | 14085 | Test set | 725 (5.1%) | ||
| R | 0.1740 | R-free | 0.2780 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.15 Å | Reflections | 14085 | Test set | 725 (5.1%) | 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 | 0.1875 | 0.2069 |
| R-free | 0.2866 | 0.2849 |
| Bond length RMS Z-score | 0.698 | 0.362 |
| Bond angle RMS Z-score | 1.047 | 0.627 |
| Model quality | ||
| Ramachandran plot normality | -3.011 16 | -1.940 31 |
| Rotamer normality | -2.640 46 | -0.957 78 |
| Coarse packing | -0.582 32 | -0.589 32 |
| Fine packing | -1.785 21 | -1.576 28 |
| Bump severity | 0.006 70 | 0.003 82 |
| Hydrogen bond satisfaction | 0.877 26 | 0.870 22 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 10 |
| Side chains flipped | 0 |
| Waters removed | 76 |
| Peptides flipped | 1 |
| Chiralities fixed | 0 |
| Residues fitting density better | 2 |
| Residues fitting density worse | 0 |