| Crystal structure of SARS-CoV 3C-like protease with C6Z |
| This entry was created with PDB-REDO version 8.13 using the deposited PDB model version 1.3 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 1 21 1 | a: 52.096 Å | b: 96.435 Å | c: 67.694 Å | α: 90.00° | β: 103.48° | γ: 90.00° |
| Resolution | 2.50 Å | Reflections | 22564 | Test set | 2000 (8.9%) | ||
| R | 0.1881 | R-free | 0.2453 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.50 Å | Reflections | 22564 | Test set | 2000 (8.9%) | ||
| Twin | false | Radiation damage | 52 | ||||
| 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 | 0.1935 | 0.1922 |
| R-free | 0.2485 | 0.2279 |
| Bond length RMS Z-score | 0.657 | 0.244 |
| Bond angle RMS Z-score | 0.718 | 0.462 |
| Model quality | ||
| Ramachandran plot normality | -3.430 13 | -1.051 54 |
| Rotamer normality | -2.938 33 | -0.212 87 |
| Coarse packing | 0.167 57 | 0.185 57 |
| Fine packing | -1.083 50 | -0.749 63 |
| Bump severity | 0.015 45 | 0.008 62 |
| Hydrogen bond satisfaction | 0.867 20 | 0.865 19 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 10 |
| Side chains flipped | 0 |
| Waters removed | 10 |
| Peptides flipped | 1 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 1 |