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| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102353 |
| This entry was created with PDB-REDO version 7.34. |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 112.157 Å | b: 52.936 Å | c: 44.403 Å | α: 90.00° | β: 103.03° | γ: 90.00° |
| Resolution | 1.69 Å | Reflections | 27616 | Test set | 1355 (4.9%) | ||
| R | 0.1930 | R-free | 0.2420 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.69 Å | Reflections | 27616 | Test set | 1355 (4.9%) | Twin | false |
| 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 | 0.1994 | 0.1938 |
| R-free | 0.2429 | 0.2462 |
| Bond length RMS Z-score | 0.634 | 0.410 |
| Bond angle RMS Z-score | 0.999 | 0.698 |
| Model quality | ||
| Ramachandran plot normality | -1.792 34 | -1.588 38 |
| Rotamer normality | -1.411 70 | -1.014 77 |
| Coarse packing | -0.334 44 | -0.294 47 |
| Fine packing | -1.642 26 | -1.476 33 |
| Bump severity | 0.005 74 | 0.004 78 |
| Hydrogen bond satisfaction | 0.885 33 | 0.893 41 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 7 |
| Side chains flipped | 0 |
| Waters removed | 80 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 3 |
| Residues fitting density worse | 0 |