This entry is not up to date with the most recent version of PDB-REDO.
Please log in
to request an update.
| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z1348371854 |
| This entry was created with PDB-REDO version 8.07. |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 112.714 Å | b: 52.798 Å | c: 52.798 Å | α: 90.00° | β: 103.05° | γ: 90.00° |
| Resolution | 1.45 Å | Reflections | 43060 | Test set | 2102 (4.9%) | ||
| R | 0.1806 | R-free | 0.2174 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.45 Å | Reflections | 43060 | Test set | 2102 (4.9%) | ||
| Twin | false | Radiation damage | 34 | ||||
| PDB-REDO files | |||||||
| Re-refined and rebuilt structure | Re-refined (only) structure |
All files
(compressed) |
|||||
| Links | |||||||
| PDBe | RCSB PDB | 3D bionotes | Proteopedia | ||||
| Original | PDB-REDO | |
|---|---|---|
| Crystallographic refinement | ||
| R | 0.1909 | 0.1860 |
| R-free | 0.2271 | 0.2265 |
| Bond length RMS Z-score | 1.294 | 0.991 |
| Bond angle RMS Z-score | 0.993 | 0.926 |
| Model quality | ||
| Ramachandran plot normality | -0.350 74 | -0.479 70 |
| Rotamer normality | -0.119 88 | 0.229 92 |
| Coarse packing | 0.559 72 | 0.482 69 |
| Fine packing | -1.519 31 | -1.545 30 |
| Bump severity | 0.005 72 | 0.008 62 |
| Hydrogen bond satisfaction | 0.891 39 | 0.889 37 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 5 |
| Side chains flipped | 0 |
| Waters removed | 40 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 1 |
| Residues fitting density worse | 0 |