| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102535 |
| 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: 112.645 Å | b: 52.876 Å | c: 44.444 Å | α: 90.00° | β: 103.13° | γ: 90.00° |
| Resolution | 1.72 Å | Reflections | 26578 | Test set | 1317 (5.0%) | ||
| R | 0.1881 | R-free | 0.2359 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.72 Å | Reflections | 26578 | Test set | 1317 (5.0%) | ||
| Twin | false | Radiation damage | 42 | ||||
| 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 | 0.1952 | 0.1950 |
| R-free | 0.2387 | 0.2384 |
| Bond length RMS Z-score | 1.265 | 0.318 |
| Bond angle RMS Z-score | 0.982 | 0.555 |
| Model quality | ||
| Ramachandran plot normality | -1.756 36 | -1.311 47 |
| Rotamer normality | -1.410 63 | -0.291 85 |
| Coarse packing | 0.523 71 | 0.546 72 |
| Fine packing | -0.454 72 | -0.397 74 |
| Bump severity | 0.006 68 | 0.010 56 |
| Hydrogen bond satisfaction | 0.875 25 | 0.869 21 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 7 |
| Side chains flipped | 0 |
| Waters removed | 63 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 1 |
| Residues fitting density worse | 0 |