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| Crystal structure (monoclinic form) of the complex resulting from the reaction between SARS-CoV-2 (2019-nCoV) main protease and tert-butyl (1-((S)-1-(((S)-4-(benzylamino)-3,4-dioxo-1-((S)-2- oxopyrrolidin-3-yl)butan-2-yl)amino)-3-cyclopropyl-1-oxopropan-2 |
| This entry was created with PDB-REDO version 8.01. |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 98.085 Å | b: 80.926 Å | c: 51.659 Å | α: 90.00° | β: 114.84° | γ: 90.00° |
| Resolution | 1.95 Å | Reflections | 26755 | Test set | 1293 (4.8%) | ||
| R | 0.1779 | R-free | 0.2191 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.95 Å | Reflections | 26755 | Test set | 1293 (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 | 0.1779 | 0.1620 |
| R-free | 0.2196 | 0.1980 |
| Bond length RMS Z-score | 0.727 | 0.656 |
| Bond angle RMS Z-score | 1.097 | 0.906 |
| Model quality | ||
| Ramachandran plot normality | -2.615 20 | -1.486 40 |
| Rotamer normality | -3.107 38 | -1.639 65 |
| Coarse packing | -0.090 57 | 0.007 62 |
| Fine packing | -1.031 52 | -0.853 59 |
| Bump severity | 0.021 38 | 0.020 39 |
| Hydrogen bond satisfaction | 0.881 29 | 0.886 34 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 11 |
| Side chains flipped | 0 |
| Waters removed | 22 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 10 |
| Residues fitting density worse | 0 |