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| Crystal structure of the complex resulting from the reaction between the SARS-CoV main protease and tert-butyl (1-((S)-3-cyclohexyl-1-(((S)-4-(cyclopropylamino)-3,4-dioxo-1-((S)-2-oxopyrrolidin-3-yl)butan-2-yl)amino)-1-oxopropan-2-yl)-2-oxo-1,2-dihydropyridin-3-yl)carbamate |
| This entry was created with PDB-REDO version 7.34. |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 107.905 Å | b: 82.247 Å | c: 53.131 Å | α: 90.00° | β: 104.46° | γ: 90.00° |
| Resolution | 1.90 Å | Reflections | 35112 | Test set | 1700 (4.8%) | ||
| R | 0.2062 | R-free | 0.2576 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.90 Å | Reflections | 35112 | Test set | 1700 (4.8%) | 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 | 0.2069 | 0.1920 |
| R-free | 0.2589 | 0.2250 |
| Bond length RMS Z-score | 0.726 | 0.659 |
| Bond angle RMS Z-score | 1.083 | 0.872 |
| Model quality | ||
| Ramachandran plot normality | -3.162 15 | -1.878 32 |
| Rotamer normality | -2.668 45 | -1.379 70 |
| Coarse packing | -0.986 16 | -0.827 22 |
| Fine packing | -1.293 41 | -1.180 45 |
| Bump severity | 0.021 38 | 0.004 78 |
| Hydrogen bond satisfaction | 0.871 22 | 0.880 28 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 6 |
| Side chains flipped | 0 |
| Waters removed | 39 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 8 |
| Residues fitting density worse | 0 |