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| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102372 |
| This entry was created with PDB-REDO version 7.34 using the deposited PDB model |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 113.335 Å | b: 53.266 Å | c: 44.411 Å | α: 90.00° | β: 103.18° | γ: 90.00° |
| Resolution | 2.32 Å | Reflections | 11232 | Test set | 576 (5.1%) | ||
| R | 0.2120 | R-free | 0.3070 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.32 Å | Reflections | 11232 | Test set | 576 (5.1%) | ||
| Twin | false | Radiation damage | N/A | ||||
| 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 | 0.2287 | 0.2467 |
| R-free | 0.3051 | 0.3301 |
| Bond length RMS Z-score | 0.667 | 0.369 |
| Bond angle RMS Z-score | 0.989 | 0.648 |
| Model quality | ||
| Ramachandran plot normality | -3.368 13 | -3.249 14 |
| Rotamer normality | -2.629 46 | -2.406 50 |
| Coarse packing | -0.780 24 | -0.806 23 |
| Fine packing | -1.873 18 | -1.976 15 |
| Bump severity | 0.008 64 | 0.011 56 |
| Hydrogen bond satisfaction | 0.851 14 | 0.858 16 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 6 |
| Side chains flipped | 0 |
| Waters removed | 77 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |