| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102432 |
| 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: 112.771 Å | b: 52.953 Å | c: 44.472 Å | α: 90.00° | β: 103.09° | γ: 90.00° |
| Resolution | 1.58 Å | Reflections | 32953 | Test set | 1628 (4.9%) | ||
| R | 0.1953 | R-free | 0.2368 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.58 Å | Reflections | 32953 | Test set | 1628 (4.9%) | ||
| Twin | false | Radiation damage | 25 | ||||
| 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 | 0.2056 | 0.2010 |
| R-free | 0.2451 | 0.2496 |
| Bond length RMS Z-score | 1.268 | 0.377 |
| Bond angle RMS Z-score | 0.974 | 0.590 |
| Model quality | ||
| Ramachandran plot normality | -1.279 48 | -1.303 47 |
| Rotamer normality | -1.272 66 | -0.377 84 |
| Coarse packing | 0.425 67 | 0.355 65 |
| Fine packing | -0.568 69 | -0.529 70 |
| Bump severity | 0.004 76 | 0.004 76 |
| Hydrogen bond satisfaction | 0.877 26 | 0.877 26 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 5 |
| Side chains flipped | 0 |
| Waters removed | 49 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |