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| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102269 |
| This entry was created with PDB-REDO version 7.36. |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 112.889 Å | b: 53.003 Å | c: 44.457 Å | α: 90.00° | β: 103.04° | γ: 90.00° |
| Resolution | 1.68 Å | Reflections | 29092 | Test set | 1441 (5.0%) | ||
| R | 0.1820 | R-free | 0.2220 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.68 Å | Reflections | 29092 | Test set | 1441 (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 | 0.1899 | 0.1963 |
| R-free | 0.2262 | 0.2306 |
| Bond length RMS Z-score | 0.667 | 0.413 |
| Bond angle RMS Z-score | 1.019 | 0.688 |
| Model quality | ||
| Ramachandran plot normality | -1.641 37 | -1.122 50 |
| Rotamer normality | -0.965 78 | -0.550 85 |
| Coarse packing | -0.284 47 | -0.262 48 |
| Fine packing | -1.551 29 | -1.354 38 |
| Bump severity | 0.020 39 | 0.011 56 |
| Hydrogen bond satisfaction | 0.882 30 | 0.866 19 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 8 |
| Side chains flipped | 0 |
| Waters removed | 62 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |