| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102739 |
| 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: 112.861 Å | b: 52.958 Å | c: 44.518 Å | α: 90.00° | β: 103.22° | γ: 90.00° |
| Resolution | 1.70 Å | Reflections | 27915 | Test set | 1387 (5.0%) | ||
| R | 0.1869 | R-free | 0.2327 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.70 Å | Reflections | 27915 | Test set | 1387 (5.0%) | ||
| Twin | false | Radiation damage | 31 | ||||
| PDB-REDO files | |||||||
| Re-refined and rebuilt structure | Re-refined (only) structure |
All files
(compressed) |
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| Links | |||||||
| PDBe | RCSB PDB | 3D bionotes | Proteopedia | ||||
| Original | PDB-REDO | |
|---|---|---|
| Crystallographic refinement | ||
| R | 0.1978 | 0.2014 |
| R-free | 0.2368 | 0.2386 |
| Bond length RMS Z-score | 1.362 | 0.424 |
| Bond angle RMS Z-score | 1.045 | 0.626 |
| Model quality | ||
| Ramachandran plot normality | -1.522 42 | -1.229 49 |
| Rotamer normality | -1.455 62 | -0.947 73 |
| Coarse packing | 0.450 68 | 0.433 68 |
| Fine packing | -0.508 71 | -0.573 69 |
| Bump severity | 0.006 68 | 0.005 72 |
| Hydrogen bond satisfaction | 0.870 22 | 0.868 21 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 6 |
| Side chains flipped | 0 |
| Waters removed | 28 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |