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| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102179 |
| This entry was created with PDB-REDO version 7.34. |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 112.038 Å | b: 52.733 Å | c: 44.717 Å | α: 90.00° | β: 103.02° | γ: 90.00° |
| Resolution | 1.76 Å | Reflections | 25084 | Test set | 1256 (5.0%) | ||
| R | 0.1800 | R-free | 0.2270 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.76 Å | Reflections | 25084 | Test set | 1256 (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 | 0.1890 | 0.2486 |
| R-free | 0.2338 | 0.2902 |
| Bond length RMS Z-score | 0.634 | 0.522 |
| Bond angle RMS Z-score | 1.003 | 0.777 |
| Model quality | ||
| Ramachandran plot normality | -1.535 39 | -1.740 35 |
| Rotamer normality | -0.893 79 | -2.342 51 |
| Coarse packing | -0.280 47 | -0.429 40 |
| Fine packing | -1.641 26 | -1.327 39 |
| Bump severity | 0.006 70 | 0.010 58 |
| Hydrogen bond satisfaction | 0.886 34 | 0.895 44 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 7 |
| Side chains flipped | 0 |
| Waters removed | 171 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 4 |