| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102274 |
| 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: 111.565 Å | b: 52.545 Å | c: 44.523 Å | α: 90.00° | β: 102.78° | γ: 90.00° |
| Resolution | 1.68 Å | Reflections | 28661 | Test set | 1417 (4.9%) | ||
| R | 0.1808 | R-free | 0.2265 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.68 Å | Reflections | 28661 | Test set | 1417 (4.9%) | ||
| Twin | false | Radiation damage | 40 | ||||
| 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 | 0.1934 | 0.1848 |
| R-free | 0.2342 | 0.2367 |
| Bond length RMS Z-score | 1.260 | 0.370 |
| Bond angle RMS Z-score | 0.978 | 0.590 |
| Model quality | ||
| Ramachandran plot normality | -1.118 52 | -1.013 55 |
| Rotamer normality | -1.222 67 | -0.378 84 |
| Coarse packing | 0.596 74 | 0.515 71 |
| Fine packing | -0.482 72 | -0.488 71 |
| Bump severity | 0.008 62 | 0.008 62 |
| Hydrogen bond satisfaction | 0.861 18 | 0.853 15 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 6 |
| Side chains flipped | 0 |
| Waters removed | 44 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 3 |
| Residues fitting density worse | 0 |