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| PanDDA analysis group deposition -- Crystal Structure of COVID-19 main protease in complex with Z219104216 |
| This entry was created with PDB-REDO version 7.34. |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 112.665 Å | b: 52.848 Å | c: 44.468 Å | α: 90.00° | β: 102.97° | γ: 90.00° |
| Resolution | 1.31 Å | Reflections | 53593 | Test set | 2605 (4.9%) | ||
| R | 0.1800 | R-free | 0.2120 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.31 Å | Reflections | 53593 | Test set | 2605 (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 | 0.2422 | 0.2000 |
| R-free | 0.2551 | 0.2202 |
| Bond length RMS Z-score | 0.657 | 0.355 |
| Bond angle RMS Z-score | 1.012 | 0.642 |
| Model quality | ||
| Ramachandran plot normality | -1.381 43 | -0.760 60 |
| Rotamer normality | -0.799 81 | 0.376 95 |
| Coarse packing | -0.254 49 | -0.169 53 |
| Fine packing | -1.512 31 | -1.427 35 |
| Bump severity | 0.005 74 | 0.002 87 |
| Hydrogen bond satisfaction | 0.884 32 | 0.879 28 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 5 |
| Side chains flipped | 0 |
| Waters removed | 26 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 90 |
| Residues fitting density worse | 0 |