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| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z2643472210 |
| This entry was created with PDB-REDO version 7.34. |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 112.634 Å | b: 52.833 Å | c: 44.441 Å | α: 90.00° | β: 103.08° | γ: 90.00° |
| Resolution | 1.52 Å | Reflections | 38237 | Test set | 1856 (4.9%) | ||
| R | 0.1770 | R-free | 0.2150 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.52 Å | Reflections | 38237 | Test set | 1856 (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 | 0.1856 | 0.2411 |
| R-free | 0.2231 | 0.2818 |
| Bond length RMS Z-score | 0.655 | 0.710 |
| Bond angle RMS Z-score | 1.023 | 0.852 |
| Model quality | ||
| Ramachandran plot normality | -1.102 50 | -1.321 44 |
| Rotamer normality | -0.784 81 | -1.527 67 |
| Coarse packing | -0.030 60 | -0.175 53 |
| Fine packing | -1.514 31 | -1.434 34 |
| Bump severity | 0.007 67 | 0.021 38 |
| Hydrogen bond satisfaction | 0.865 19 | 0.894 43 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 9 |
| Side chains flipped | 0 |
| Waters removed | 64 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 19 |