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| Structure of SARS coronavirus main protease in complex with the alpha-ketoamide (S)-N-benzyl-3-((S)-2-cinnamamido-3-cyclopropylpropanamido)-2-oxo-4-((S)-2-oxopyrrolidin-3-yl)butanamide (Cinnamoyl-cyclopropylalanine-GlnLactam-CO-CO-NH-benzyl) |
| This entry was created with PDB-REDO version 7.15. |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 109.165 Å | b: 81.873 Å | c: 53.499 Å | α: 90.00° | β: 104.34° | γ: 90.00° |
| Resolution | 2.00 Å | Reflections | 30288 | Test set | 1501 (5.0%) | ||
| R | 0.1920 | R-free | 0.2520 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.00 Å | Reflections | 30288 | Test set | 1501 (5.0%) | Twin | false |
| 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 | 0.1922 | 0.1806 |
| R-free | 0.2515 | 0.2209 |
| Bond length RMS Z-score | 0.895 | 0.783 |
| Bond angle RMS Z-score | 0.964 | 0.858 |
| Model quality | ||
| Ramachandran plot normality | -1.470 41 | -0.964 54 |
| Rotamer normality | -2.477 49 | -1.838 61 |
| Coarse packing | -1.156 12 | -1.031 15 |
| Fine packing | -1.541 30 | -1.372 37 |
| Bump severity | 0.002 87 | 0.005 74 |
| Hydrogen bond satisfaction | 0.890 38 | 0.878 27 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 3 |
| Side chains flipped | 1 |
| Waters removed | 20 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 21 |
| Residues fitting density worse | 0 |