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| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z24758179 |
| This entry was created with PDB-REDO version 7.34. |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 112.514 Å | b: 52.708 Å | c: 44.455 Å | α: 90.00° | β: 103.04° | γ: 90.00° |
| Resolution | 1.61 Å | Reflections | 31983 | Test set | 1584 (5.0%) | ||
| R | 0.1980 | R-free | 0.2460 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.61 Å | Reflections | 31983 | Test set | 1584 (5.0%) | 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 | 0.2121 | 0.2062 |
| R-free | 0.2578 | 0.2568 |
| Bond length RMS Z-score | 0.681 | 0.595 |
| Bond angle RMS Z-score | 1.001 | 0.777 |
| Model quality | ||
| Ramachandran plot normality | -2.006 29 | -1.837 33 |
| Rotamer normality | -1.483 68 | -0.886 79 |
| Coarse packing | -0.363 43 | -0.395 41 |
| Fine packing | -1.454 34 | -1.474 33 |
| Bump severity | 0.004 78 | 0.019 41 |
| Hydrogen bond satisfaction | 0.878 27 | 0.891 39 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 8 |
| Side chains flipped | 0 |
| Waters removed | 64 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 2 |
| Residues fitting density worse | 0 |