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 Z44592329 |
| This entry was created with PDB-REDO version 8.07 using the deposited PDB model version 2.4 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 112.267 Å | b: 52.583 Å | c: 52.583 Å | α: 90.00° | β: 102.95° | γ: 90.00° |
| Resolution | 1.58 Å | Reflections | 34609 | Test set | 1714 (5.0%) | ||
| R | 0.1758 | R-free | 0.2149 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.58 Å | Reflections | 34609 | Test set | 1714 (5.0%) | ||
| Twin | false | Radiation damage | 18 | ||||
| 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 | 0.1845 | 0.1810 |
| R-free | 0.2221 | 0.2246 |
| Bond length RMS Z-score | 1.313 | 0.509 |
| Bond angle RMS Z-score | 1.011 | 0.663 |
| Model quality | ||
| Ramachandran plot normality | -1.029 55 | -0.813 61 |
| Rotamer normality | -1.466 62 | -0.546 81 |
| Coarse packing | 0.541 72 | 0.482 69 |
| Fine packing | -1.534 30 | -1.436 34 |
| Bump severity | 0.009 59 | 0.011 54 |
| Hydrogen bond satisfaction | 0.891 39 | 0.907 59 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 5 |
| Side chains flipped | 0 |
| Waters removed | 56 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 3 |
| Residues fitting density worse | 0 |