| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102281 |
| 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: 112.332 Å | b: 52.696 Å | c: 44.479 Å | α: 90.00° | β: 102.87° | γ: 90.00° |
| Resolution | 1.65 Å | Reflections | 30014 | Test set | 1480 (4.9%) | ||
| R | 0.1814 | R-free | 0.2263 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.65 Å | Reflections | 30014 | Test set | 1480 (4.9%) | ||
| Twin | false | Radiation damage | 13 | ||||
| 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 | 0.1911 | 0.1886 |
| R-free | 0.2348 | 0.2335 |
| Bond length RMS Z-score | 1.280 | 0.367 |
| Bond angle RMS Z-score | 0.977 | 0.584 |
| Model quality | ||
| Ramachandran plot normality | -1.311 47 | -1.285 48 |
| Rotamer normality | -0.664 79 | 0.433 94 |
| Coarse packing | 0.539 72 | 0.480 69 |
| Fine packing | -0.433 73 | -0.373 75 |
| Bump severity | 0.003 81 | 0.004 76 |
| Hydrogen bond satisfaction | 0.881 29 | 0.876 26 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 8 |
| Side chains flipped | 0 |
| Waters removed | 36 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |