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| Crystal structure (orthorhombic 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 |
| This entry was created with PDB-REDO version 8.01. |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 21 21 21 | a: 68.566 Å | b: 101.602 Å | c: 103.696 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
| Resolution | 2.20 Å | Reflections | 37448 | Test set | 1898 (5.1%) | ||
| R | 0.1862 | R-free | 0.2473 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.20 Å | Reflections | 37448 | Test set | 1898 (5.1%) | 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 | 0.1864 | 0.1815 |
| R-free | 0.2478 | 0.2336 |
| Bond length RMS Z-score | 0.790 | 0.475 |
| Bond angle RMS Z-score | 1.157 | 0.788 |
| Model quality | ||
| Ramachandran plot normality | -2.899 17 | -1.262 46 |
| Rotamer normality | -2.845 42 | -1.357 71 |
| Coarse packing | -0.278 47 | -0.057 59 |
| Fine packing | -1.957 15 | -1.614 27 |
| Bump severity | 0.012 53 | 0.027 32 |
| Hydrogen bond satisfaction | 0.881 29 | 0.883 31 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 25 |
| Side chains flipped | 0 |
| Waters removed | 23 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 4 |
| Residues fitting density worse | 0 |