| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102306 |
| This entry was created with PDB-REDO version 8.13 using the deposited PDB model version 1.5 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 112.254 Å | b: 52.664 Å | c: 44.535 Å | α: 90.00° | β: 103.02° | γ: 90.00° |
| Resolution | 1.48 Å | Reflections | 40622 | Test set | 1979 (4.9%) | ||
| R | 0.1873 | R-free | 0.2236 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.48 Å | Reflections | 40622 | Test set | 1979 (4.9%) | ||
| Twin | false | Radiation damage | 12 | ||||
| PDB-REDO files | |||||||
| Re-refined and rebuilt structure | Re-refined (only) structure |
All files
(compressed) |
|||||
| Links | |||||||
| PDBe | RCSB PDB | 3D bionotes | Proteopedia | ||||
| Original | PDB-REDO | |
|---|---|---|
| Crystallographic refinement | ||
| R | 0.1954 | 0.1974 |
| R-free | 0.2300 | 0.2274 |
| Bond length RMS Z-score | 1.284 | 0.352 |
| Bond angle RMS Z-score | 0.998 | 0.589 |
| Model quality | ||
| Ramachandran plot normality | -1.021 55 | -0.928 57 |
| Rotamer normality | -0.635 79 | 0.218 92 |
| Coarse packing | 0.523 71 | 0.446 68 |
| Fine packing | -0.524 70 | -0.454 72 |
| Bump severity | 0.003 81 | 0.011 54 |
| Hydrogen bond satisfaction | 0.880 29 | 0.879 28 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 4 |
| Side chains flipped | 0 |
| Waters removed | 37 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |