| Crystal structure of SARS-CoV 3C-like protease with M4Z |
| 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: 52.317 Å | b: 96.492 Å | c: 67.644 Å | α: 90.00° | β: 103.31° | γ: 90.00° |
| Resolution | 1.95 Å | Reflections | 46899 | Test set | 2000 (4.3%) | ||
| R | 0.1875 | R-free | 0.2304 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.95 Å | Reflections | 46899 | Test set | 2000 (4.3%) | ||
| Twin | false | Radiation damage | 48 | ||||
| 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 | 0.1877 | 0.1716 |
| R-free | 0.2296 | 0.2052 |
| Bond length RMS Z-score | 0.626 | 0.353 |
| Bond angle RMS Z-score | 0.714 | 0.570 |
| Model quality | ||
| Ramachandran plot normality | -1.632 39 | -0.732 63 |
| Rotamer normality | -0.948 73 | 0.019 90 |
| Coarse packing | 0.341 64 | 0.417 67 |
| Fine packing | -0.597 68 | -0.477 72 |
| Bump severity | 0.010 56 | 0.020 37 |
| Hydrogen bond satisfaction | 0.874 24 | 0.877 26 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 11 |
| Side chains flipped | 0 |
| Waters removed | 22 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 5 |
| Residues fitting density worse | 0 |