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| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102739 |
| This entry was created with PDB-REDO version 7.34. |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 112.861 Å | b: 52.958 Å | c: 44.518 Å | α: 90.00° | β: 103.22° | γ: 90.00° |
| Resolution | 1.70 Å | Reflections | 27915 | Test set | 1387 (5.0%) | ||
| R | 0.1870 | R-free | 0.2330 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.70 Å | Reflections | 27915 | Test set | 1387 (5.0%) | ||
| 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 | 0.1976 | 0.1990 |
| R-free | 0.2370 | 0.2355 |
| Bond length RMS Z-score | 0.714 | 0.415 |
| Bond angle RMS Z-score | 1.074 | 0.693 |
| Model quality | ||
| Ramachandran plot normality | -1.843 33 | -1.494 40 |
| Rotamer normality | -1.454 69 | -0.688 83 |
| Coarse packing | -0.289 47 | -0.277 47 |
| Fine packing | -1.709 23 | -1.594 28 |
| Bump severity | 0.008 64 | 0.005 74 |
| Hydrogen bond satisfaction | 0.879 28 | 0.894 43 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 9 |
| Side chains flipped | 0 |
| Waters removed | 32 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 1 |
| Residues fitting density worse | 0 |