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| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z1741969146 |
| 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: 112.671 Å | b: 52.715 Å | c: 52.715 Å | α: 90.00° | β: 102.96° | γ: 90.00° |
| Resolution | 1.53 Å | Reflections | 37976 | Test set | 1847 (4.9%) | ||
| R | 0.1817 | R-free | 0.2216 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.53 Å | Reflections | 37976 | Test set | 1847 (4.9%) | ||
| Twin | false | Radiation damage | 57 | ||||
| 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 | 0.1901 | 0.1890 |
| R-free | 0.2276 | 0.2245 |
| Bond length RMS Z-score | 1.316 | 0.537 |
| Bond angle RMS Z-score | 0.975 | 0.682 |
| Model quality | ||
| Ramachandran plot normality | -0.599 67 | -0.661 65 |
| Rotamer normality | -0.662 79 | -0.167 87 |
| Coarse packing | 0.409 67 | 0.359 65 |
| Fine packing | -1.687 24 | -1.427 35 |
| Bump severity | 0.003 81 | 0.010 56 |
| Hydrogen bond satisfaction | 0.888 36 | 0.875 25 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 7 |
| Side chains built | 0 |
| Waters removed | 41 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |