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| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z1220452176 |
| This entry was created with PDB-REDO version 7.36. |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 112.090 Å | b: 52.513 Å | c: 44.384 Å | α: 90.00° | β: 102.94° | γ: 90.00° |
| Resolution | 1.59 Å | Reflections | 33532 | Test set | 1657 (4.9%) | ||
| R | 0.1900 | R-free | 0.2330 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.59 Å | Reflections | 33532 | Test set | 1657 (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 | 0.2119 | 0.3089 |
| R-free | 0.2555 | 0.3505 |
| Bond length RMS Z-score | 0.654 | 0.638 |
| Bond angle RMS Z-score | 1.012 | 0.819 |
| Model quality | ||
| Ramachandran plot normality | -1.669 36 | -2.109 28 |
| Rotamer normality | -1.235 73 | -2.255 53 |
| Coarse packing | -0.158 54 | -0.373 42 |
| Fine packing | -1.441 34 | -1.443 34 |
| Bump severity | 0.007 67 | 0.026 33 |
| Hydrogen bond satisfaction | 0.881 29 | 0.869 21 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 6 |
| Side chains flipped | 0 |
| Waters removed | 80 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 34 |