| 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 8.12 using the deposited PDB model version 1.2 |
| 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 | 0.1922 | R-free | 0.2515 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.00 Å | Reflections | 30288 | Test set | 1501 (5.0%) | ||
| Twin | false | Radiation damage | 42 | ||||
| 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 | 0.1939 | 0.1804 |
| R-free | 0.2516 | 0.2259 |
| Bond length RMS Z-score | 1.595 | 0.690 |
| Bond angle RMS Z-score | 1.300 | 0.781 |
| Model quality | ||
| Ramachandran plot normality | -2.053 30 | -1.537 41 |
| Rotamer normality | -1.826 54 | -1.437 63 |
| Coarse packing | -0.510 27 | -0.379 32 |
| Fine packing | -0.726 64 | -0.722 64 |
| Bump severity | 0.002 85 | 0.008 62 |
| Hydrogen bond satisfaction | 0.867 20 | 0.868 21 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 9 |
| Side chains flipped | 0 |
| Waters removed | 27 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 3 |
| Residues fitting density worse | 0 |