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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 8.07 using the deposited PDB model version 1.5 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 111.317 Å | b: 52.414 Å | c: 52.414 Å | α: 90.00° | β: 102.95° | γ: 90.00° |
| Resolution | 1.67 Å | Reflections | 27298 | Test set | 1351 (4.9%) | ||
| R | 0.1792 | R-free | 0.2272 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.67 Å | Reflections | 27298 | Test set | 1351 (4.9%) | ||
| Twin | false | Radiation damage | 6 | ||||
| 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 | 0.1999 | 0.1876 |
| R-free | 0.2409 | 0.2405 |
| Bond length RMS Z-score | 1.397 | 0.412 |
| Bond angle RMS Z-score | 0.966 | 0.606 |
| Model quality | ||
| Ramachandran plot normality | -1.282 48 | -1.150 51 |
| Rotamer normality | -0.661 79 | 0.079 91 |
| Coarse packing | 0.679 76 | 0.688 77 |
| Fine packing | -1.502 32 | -1.327 39 |
| Bump severity | 0.004 76 | 0.006 68 |
| Hydrogen bond satisfaction | 0.858 16 | 0.844 12 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 7 |
| Side chains flipped | 0 |
| Waters removed | 73 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 2 |
| Residues fitting density worse | 0 |