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| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z2856434836 |
| This entry was created with PDB-REDO version 7.34. |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 112.706 Å | b: 52.645 Å | c: 44.480 Å | α: 90.00° | β: 102.87° | γ: 90.00° |
| Resolution | 1.72 Å | Reflections | 26626 | Test set | 1312 (4.9%) | ||
| R | 0.1670 | R-free | 0.2250 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.72 Å | Reflections | 26626 | Test set | 1312 (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 | 0.2027 | 0.1999 |
| R-free | 0.2517 | 0.2518 |
| Bond length RMS Z-score | 0.653 | 0.412 |
| Bond angle RMS Z-score | 1.011 | 0.692 |
| Model quality | ||
| Ramachandran plot normality | -1.280 45 | -1.016 53 |
| Rotamer normality | -1.396 70 | -0.771 81 |
| Coarse packing | -0.286 47 | -0.354 43 |
| Fine packing | -1.628 26 | -1.428 35 |
| Bump severity | 0.011 56 | 0.015 47 |
| Hydrogen bond satisfaction | 0.830 9 | 0.844 12 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 8 |
| Side chains flipped | 0 |
| Waters removed | 124 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 2 |
| Residues fitting density worse | 0 |