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| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z1545313172 |
| This entry was created with PDB-REDO version 7.34. |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 111.317 Å | b: 52.414 Å | c: 44.278 Å | α: 90.00° | β: 102.95° | γ: 90.00° |
| Resolution | 1.67 Å | Reflections | 27298 | Test set | 1351 (4.9%) | ||
| R | 0.1790 | R-free | 0.2270 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.67 Å | Reflections | 27298 | Test set | 1351 (4.9%) | Twin | false |
| 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 | 0.2001 | 0.1894 |
| R-free | 0.2411 | 0.2439 |
| Bond length RMS Z-score | 0.625 | 0.415 |
| Bond angle RMS Z-score | 1.019 | 0.695 |
| Model quality | ||
| Ramachandran plot normality | -1.498 40 | -1.323 44 |
| Rotamer normality | -0.660 83 | -0.402 87 |
| Coarse packing | -0.109 56 | -0.073 58 |
| Fine packing | -1.441 34 | -1.251 42 |
| Bump severity | 0.004 78 | 0.006 70 |
| Hydrogen bond satisfaction | 0.863 18 | 0.846 12 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 8 |
| Side chains flipped | 0 |
| Waters removed | 77 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 2 |
| Residues fitting density worse | 0 |