| 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 8.13 using the deposited PDB model version 1.4 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 107.905 Å | b: 82.247 Å | c: 53.131 Å | α: 90.00° | β: 104.47° | 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 | Radiation damage | 16 | ||||
| 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 | 0.2075 | 0.2078 |
| R-free | 0.2584 | 0.2634 |
| Bond length RMS Z-score | 1.441 | 0.365 |
| Bond angle RMS Z-score | 1.171 | 0.596 |
| Model quality | ||
| Ramachandran plot normality | -2.831 19 | -2.477 23 |
| Rotamer normality | -2.670 38 | -1.411 63 |
| Coarse packing | -0.263 37 | -0.234 38 |
| Fine packing | -0.676 65 | -0.682 65 |
| Bump severity | 0.005 72 | 0.011 54 |
| Hydrogen bond satisfaction | 0.856 16 | 0.861 18 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 7 |
| Side chains flipped | 0 |
| Waters removed | 26 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 2 |
| Residues fitting density worse | 0 |