| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z54571979 |
| This entry was created with PDB-REDO version 8.20 using the deposited PDB model version 1.6 |
| From original header | |||||
|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 112.560Å b: 52.810Å c: 44.620Å | α: 90.00° β: 103.20° γ: 90.00° | ||
| Resolution | 1.87 Å | Reflections | 21169 | Test set | 1077 (5.1%) |
| R | 0.1857 | R-free | 0.2505 | ||
| According to PDB-REDO | |||||
| Resolution | 1.87 Å | Reflections | 21169 | Test set | 1077 (5.1%) |
| Twin | false | Radiation damage | 19 | ||
| PDB-REDO files | |||||
| Re-refined and rebuilt structure | Re-refined (only) structure |
All files
(compressed) |
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| Links | |||||
| PDBe | RCSB PDB | Proteopedia | |||
| Original | PDB-REDO | |
|---|---|---|
| Crystallographic refinement | ||
| R | 0.1955 | 0.2092 |
| R-free | 0.2564 | 0.2604 |
| Bond length RMS Z-score | 1.340 | 0.195 |
| Bond angle RMS Z-score | 1.029 | 0.442 |
| Model quality | ||
| Ramachandran plot normality | -1.514 42 | -1.056 54 |
| Rotamer normality | -1.849 54 | -0.414 83 |
| Coarse packing | 0.387 66 | 0.294 62 |
| Fine packing | -0.557 69 | -0.508 71 |
| MolProbity Clashscore | 4.850 54 | 4.000 63 |
| Hydrogen bond satisfaction | 0.876 26 | 0.877 26 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | N/A |
| Side chains built | 0 |
| Waters removed | N/A |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |