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| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102201 |
| This entry was created with PDB-REDO version 7.36 using the deposited PDB model |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 112.074 Å | b: 52.597 Å | c: 44.389 Å | α: 90.00° | β: 102.86° | γ: 90.00° |
| Resolution | 1.81 Å | Reflections | 23004 | Test set | 1162 (5.1%) | ||
| R | 0.1780 | R-free | 0.2310 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.81 Å | Reflections | 23004 | Test set | 1162 (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 | 0.1872 | 0.2401 |
| R-free | 0.2340 | 0.2828 |
| Bond length RMS Z-score | 0.654 | 0.540 |
| Bond angle RMS Z-score | 1.033 | 0.808 |
| Model quality | ||
| Ramachandran plot normality | -1.760 34 | -1.773 34 |
| Rotamer normality | -1.176 74 | -2.057 57 |
| Coarse packing | -0.229 50 | -0.297 46 |
| Fine packing | -1.615 27 | -1.276 41 |
| Bump severity | 0.009 61 | 0.015 47 |
| Hydrogen bond satisfaction | 0.889 37 | 0.881 29 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 3 |
| Side chains flipped | 0 |
| Waters removed | 128 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 2 |