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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 8.07 using the deposited PDB model version 1.5 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 113.429 Å | b: 53.057 Å | c: 53.057 Å | α: 90.00° | β: 103.10° | γ: 90.00° |
| Resolution | 1.44 Å | Reflections | 45870 | Test set | 2231 (4.9%) | ||
| R | 0.1773 | R-free | 0.2132 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.44 Å | Reflections | 45870 | Test set | 2231 (4.9%) | ||
| Twin | false | Radiation damage | 11 | ||||
| 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 | 0.1858 | 0.1880 |
| R-free | 0.2231 | 0.2211 |
| Bond length RMS Z-score | 1.360 | 0.400 |
| Bond angle RMS Z-score | 1.029 | 0.615 |
| Model quality | ||
| Ramachandran plot normality | -0.262 76 | -0.187 78 |
| Rotamer normality | -0.258 86 | 0.591 95 |
| Coarse packing | 0.317 63 | 0.232 60 |
| Fine packing | -1.666 25 | -1.562 29 |
| Bump severity | 0.005 72 | 0.002 85 |
| Hydrogen bond satisfaction | 0.883 31 | 0.896 45 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 6 |
| Side chains flipped | 0 |
| Waters removed | 46 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |