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| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z54571979 |
| This entry was created with PDB-REDO version 7.34. |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 112.560 Å | b: 52.810 Å | c: 44.620 Å | α: 90.00° | β: 103.20° | γ: 90.00° |
| Resolution | 1.87 Å | Reflections | 21169 | Test set | 1077 (5.1%) | ||
| R | 0.1860 | R-free | 0.2510 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.87 Å | Reflections | 21169 | Test set | 1077 (5.1%) | 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 | 0.1956 | 0.2143 |
| R-free | 0.2568 | 0.2614 |
| Bond length RMS Z-score | 0.686 | 0.342 |
| Bond angle RMS Z-score | 1.044 | 0.612 |
| Model quality | ||
| Ramachandran plot normality | -1.724 35 | -1.678 36 |
| Rotamer normality | -1.849 61 | -0.125 91 |
| Coarse packing | -0.372 42 | -0.486 37 |
| Fine packing | -1.627 26 | -1.384 37 |
| Bump severity | 0.003 82 | 0.002 87 |
| Hydrogen bond satisfaction | 0.891 39 | 0.897 46 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 6 |
| Side chains flipped | 0 |
| Waters removed | 53 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |