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| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z1271660837 |
| This entry was created with PDB-REDO version 7.34. |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 112.489 Å | b: 52.630 Å | c: 44.593 Å | α: 90.00° | β: 102.98° | γ: 90.00° |
| Resolution | 1.48 Å | Reflections | 40538 | Test set | 2001 (4.9%) | ||
| R | 0.1830 | R-free | 0.2240 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.48 Å | Reflections | 40538 | Test set | 2001 (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 | 0.1908 | 0.2712 |
| R-free | 0.2313 | 0.3043 |
| Bond length RMS Z-score | 0.661 | 0.799 |
| Bond angle RMS Z-score | 1.020 | 0.963 |
| Model quality | ||
| Ramachandran plot normality | -1.113 50 | -2.160 27 |
| Rotamer normality | -0.256 89 | -2.320 52 |
| Coarse packing | -0.170 53 | -0.330 45 |
| Fine packing | -1.486 32 | -0.837 59 |
| Bump severity | 0.005 74 | 0.013 51 |
| Hydrogen bond satisfaction | 0.893 41 | 0.884 32 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 8 |
| Side chains flipped | 0 |
| Waters removed | 270 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 53 |