| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102201 |
| 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: 112.074 Å | b: 52.597 Å | c: 44.389 Å | α: 90.00° | β: 102.86° | γ: 90.00° |
| Resolution | 1.81 Å | Reflections | 23004 | Test set | 1162 (5.1%) | ||
| R | 0.1783 | R-free | 0.2311 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.81 Å | Reflections | 23004 | Test set | 1162 (5.1%) | ||
| Twin | false | Radiation damage | 32 | ||||
| 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 | 0.1873 | 0.1885 |
| R-free | 0.2332 | 0.2281 |
| Bond length RMS Z-score | 1.276 | 0.305 |
| Bond angle RMS Z-score | 0.989 | 0.539 |
| Model quality | ||
| Ramachandran plot normality | -1.595 40 | -1.455 43 |
| Rotamer normality | -1.175 68 | -0.516 82 |
| Coarse packing | 0.495 70 | 0.461 69 |
| Fine packing | -0.600 68 | -0.477 72 |
| Bump severity | 0.008 62 | 0.012 51 |
| Hydrogen bond satisfaction | 0.876 26 | 0.877 26 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 8 |
| Side chains flipped | 0 |
| Waters removed | 48 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |