| Structure of SARS coronavirus main protease in complex with the alpha-ketoamide (S)-N-benzyl-3-((S)-2-cinnamamido-3-phenylpropanamido)-2-oxo-4-((S)-2-oxopyrrolidin-3-yl)butanamide |
| This entry was created with PDB-REDO version 8.12 using the deposited PDB model version 2.1 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 108.196 Å | b: 82.284 Å | c: 53.435 Å | α: 90.00° | β: 103.95° | γ: 90.00° |
| Resolution | 1.62 Å | Reflections | 56524 | Test set | 2869 (5.1%) | ||
| R | 0.1725 | R-free | 0.2005 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.62 Å | Reflections | 56524 | Test set | 2869 (5.1%) | ||
| Twin | false | Radiation damage | 81 | ||||
| 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 | 0.1735 | 0.1645 |
| R-free | 0.2001 | 0.1895 |
| Bond length RMS Z-score | 2.098 | 0.806 |
| Bond angle RMS Z-score | 1.467 | 0.844 |
| Model quality | ||
| Ramachandran plot normality | -1.163 51 | -0.661 65 |
| Rotamer normality | -0.985 72 | 0.067 90 |
| Coarse packing | -0.072 45 | -0.011 48 |
| Fine packing | -0.536 70 | -0.466 72 |
| Bump severity | 0.011 54 | 0.012 51 |
| Hydrogen bond satisfaction | 0.886 34 | 0.884 32 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 5 |
| Side chains flipped | 0 |
| Waters removed | 83 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 4 |
| Residues fitting density worse | 1 |