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| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z217038356 |
| This entry was created with PDB-REDO version 7.34. |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 111.967 Å | b: 52.499 Å | c: 44.563 Å | α: 90.00° | β: 102.92° | γ: 90.00° |
| Resolution | 1.43 Å | Reflections | 44145 | Test set | 2146 (4.9%) | ||
| R | 0.1820 | R-free | 0.2150 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.43 Å | Reflections | 44145 | Test set | 2146 (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 | 0.1939 | 0.1893 |
| R-free | 0.2303 | 0.2333 |
| Bond length RMS Z-score | 0.649 | 0.430 |
| Bond angle RMS Z-score | 1.011 | 0.696 |
| Model quality | ||
| Ramachandran plot normality | -0.936 55 | -0.842 58 |
| Rotamer normality | -0.903 79 | -0.287 89 |
| Coarse packing | -0.193 52 | -0.173 53 |
| Fine packing | -1.558 29 | -1.401 36 |
| Bump severity | 0.006 70 | 0.006 70 |
| Hydrogen bond satisfaction | 0.894 43 | 0.901 52 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 8 |
| Side chains flipped | 0 |
| Waters removed | 50 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 4 |
| Residues fitting density worse | 0 |