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| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z271004858 |
| This entry was created with PDB-REDO version 7.34. |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 113.429 Å | b: 53.057 Å | c: 44.674 Å | α: 90.00° | β: 103.10° | γ: 90.00° |
| Resolution | 1.44 Å | Reflections | 45870 | Test set | 2231 (4.9%) | ||
| R | 0.1770 | R-free | 0.2130 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.44 Å | Reflections | 45870 | Test set | 2231 (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 | 0.1860 | 0.2261 |
| R-free | 0.2236 | 0.2571 |
| Bond length RMS Z-score | 0.695 | 0.723 |
| Bond angle RMS Z-score | 1.032 | 0.916 |
| Model quality | ||
| Ramachandran plot normality | -0.614 64 | -0.688 62 |
| Rotamer normality | -0.258 89 | -0.714 82 |
| Coarse packing | -0.380 42 | -0.461 38 |
| Fine packing | -1.517 31 | -1.469 33 |
| Bump severity | 0.005 74 | 0.004 78 |
| Hydrogen bond satisfaction | 0.910 64 | 0.889 37 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 6 |
| Side chains flipped | 0 |
| Waters removed | 13 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 14 |