| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102575 |
| 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: 112.854 Å | b: 52.919 Å | c: 44.942 Å | α: 90.00° | β: 103.14° | γ: 90.00° |
| Resolution | 1.75 Å | Reflections | 25961 | Test set | 1294 (5.0%) | ||
| R | 0.1875 | R-free | 0.2348 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.75 Å | Reflections | 25961 | Test set | 1294 (5.0%) | ||
| Twin | false | Radiation damage | 50 | ||||
| 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 | 0.1971 | 0.2017 |
| R-free | 0.2394 | 0.2384 |
| Bond length RMS Z-score | 1.320 | 0.243 |
| Bond angle RMS Z-score | 0.986 | 0.491 |
| Model quality | ||
| Ramachandran plot normality | -1.566 40 | -1.195 50 |
| Rotamer normality | -1.547 60 | -0.312 85 |
| Coarse packing | 0.178 57 | 0.102 54 |
| Fine packing | -0.816 60 | -0.805 61 |
| Bump severity | 0.003 81 | 0.011 54 |
| Hydrogen bond satisfaction | 0.869 21 | 0.875 25 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 9 |
| Side chains flipped | 0 |
| Waters removed | 49 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |