| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102704 |
| 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: 112.943 Å | b: 52.908 Å | c: 44.529 Å | α: 90.00° | β: 103.09° | γ: 90.00° |
| Resolution | 1.78 Å | Reflections | 24602 | Test set | 1226 (5.0%) | ||
| R | 0.1920 | R-free | 0.2474 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.78 Å | Reflections | 24602 | Test set | 1226 (5.0%) | ||
| Twin | false | Radiation damage | 37 | ||||
| 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 | 0.2101 | 0.2098 |
| R-free | 0.2595 | 0.2533 |
| Bond length RMS Z-score | 1.287 | 0.193 |
| Bond angle RMS Z-score | 0.963 | 0.456 |
| Model quality | ||
| Ramachandran plot normality | -1.808 35 | -1.427 44 |
| Rotamer normality | -1.373 64 | -0.382 84 |
| Coarse packing | 0.396 66 | 0.298 62 |
| Fine packing | -0.626 67 | -0.511 71 |
| Bump severity | 0.009 59 | 0.017 42 |
| Hydrogen bond satisfaction | 0.873 24 | 0.869 21 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 7 |
| Side chains flipped | 0 |
| Waters removed | 28 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |