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| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z18197050 |
| This entry was created with PDB-REDO version 7.34. |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 112.891 Å | b: 53.030 Å | c: 44.352 Å | α: 90.00° | β: 102.46° | γ: 90.00° |
| Resolution | 1.93 Å | Reflections | 19175 | Test set | 991 (5.2%) | ||
| R | 0.1730 | R-free | 0.2350 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.93 Å | Reflections | 19175 | Test set | 991 (5.2%) | 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 | 0.1824 | 0.1905 |
| R-free | 0.2418 | 0.2472 |
| Bond length RMS Z-score | 0.653 | 0.487 |
| Bond angle RMS Z-score | 1.027 | 0.729 |
| Model quality | ||
| Ramachandran plot normality | -1.937 31 | -1.655 36 |
| Rotamer normality | -2.144 55 | -1.684 64 |
| Coarse packing | -0.262 48 | -0.280 47 |
| Fine packing | -1.418 35 | -1.120 48 |
| Bump severity | 0.006 70 | 0.013 51 |
| Hydrogen bond satisfaction | 0.875 25 | 0.890 38 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 5 |
| Side chains flipped | 0 |
| Waters removed | 121 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |