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| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z2856434865 |
| This entry was created with PDB-REDO version 8.07. |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 113.307 Å | b: 52.912 Å | c: 52.912 Å | α: 90.00° | β: 103.01° | γ: 90.00° |
| Resolution | 1.47 Å | Reflections | 41453 | Test set | 2028 (4.9%) | ||
| R | 0.1814 | R-free | 0.2112 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.47 Å | Reflections | 41453 | Test set | 2028 (4.9%) | ||
| Twin | false | Radiation damage | 3 | ||||
| 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 | 0.2031 | 0.2021 |
| R-free | 0.2266 | 0.2277 |
| Bond length RMS Z-score | 1.329 | 0.572 |
| Bond angle RMS Z-score | 1.019 | 0.713 |
| Model quality | ||
| Ramachandran plot normality | -0.287 76 | -0.276 76 |
| Rotamer normality | -0.403 84 | 0.162 92 |
| Coarse packing | 0.391 66 | 0.314 63 |
| Fine packing | -1.548 30 | -1.484 32 |
| Bump severity | 0.002 85 | 0.008 62 |
| Hydrogen bond satisfaction | 0.876 26 | 0.859 17 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 4 |
| Side chains flipped | 0 |
| Waters removed | 80 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |