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| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z2856434856 |
| This entry was created with PDB-REDO version 8.07 using the deposited PDB model version 1.5 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 113.646 Å | b: 53.228 Å | c: 53.228 Å | α: 90.00° | β: 102.99° | γ: 90.00° |
| Resolution | 1.82 Å | Reflections | 23219 | Test set | 1163 (5.0%) | ||
| R | 0.1832 | R-free | 0.2401 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.82 Å | Reflections | 23219 | Test set | 1163 (5.0%) | ||
| Twin | false | Radiation damage | 48 | ||||
| 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 | 0.1880 | 0.1821 |
| R-free | 0.2420 | 0.2386 |
| Bond length RMS Z-score | 1.388 | 0.720 |
| Bond angle RMS Z-score | 0.989 | 0.822 |
| Model quality | ||
| Ramachandran plot normality | -1.612 39 | -1.386 45 |
| Rotamer normality | -1.651 58 | -1.317 65 |
| Coarse packing | 0.336 64 | 0.348 64 |
| Fine packing | -1.670 25 | -1.446 34 |
| Bump severity | 0.011 54 | 0.020 37 |
| Hydrogen bond satisfaction | 0.881 29 | 0.897 46 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 12 |
| Side chains flipped | 0 |
| Waters removed | 67 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 2 |
| Residues fitting density worse | 0 |