| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102243 |
| 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: 112.828 Å | b: 53.056 Å | c: 44.493 Å | α: 90.00° | β: 103.19° | γ: 90.00° |
| Resolution | 1.43 Å | Reflections | 46157 | Test set | 2235 (4.8%) | ||
| R | 0.1895 | R-free | 0.2232 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.43 Å | Reflections | 46157 | Test set | 2235 (4.8%) | ||
| Twin | false | Radiation damage | 6 | ||||
| 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 | 0.2073 | 0.2056 |
| R-free | 0.2404 | 0.2334 |
| Bond length RMS Z-score | 1.277 | 0.302 |
| Bond angle RMS Z-score | 1.047 | 0.564 |
| Model quality | ||
| Ramachandran plot normality | -0.592 67 | -0.461 71 |
| Rotamer normality | -0.900 74 | 0.037 90 |
| Coarse packing | 0.462 69 | 0.490 70 |
| Fine packing | -0.512 71 | -0.410 74 |
| Bump severity | 0.004 76 | 0.005 72 |
| Hydrogen bond satisfaction | 0.860 17 | 0.866 20 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 7 |
| Side chains flipped | 0 |
| Waters removed | 30 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |