| 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-2-yl)-2-oxo-1,2-dihydropyridin-3-yl)carbamate (alpha-ketoamide 13b) |
| This entry was created with PDB-REDO version 8.13 using the deposited PDB model version 3.1 |
| 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 | 0.1890 | R-free | 0.2343 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.20 Å | Reflections | 37448 | Test set | 1898 (5.1%) | ||
| Twin | false | Radiation damage | 65 | ||||
| PDB-REDO files | |||||||
| Re-refined and rebuilt structure | Re-refined (only) structure |
All files
(compressed) |
|||||
| Links | |||||||
| PDBe | RCSB PDB | 3D bionotes | Proteopedia | ||||
| Original | PDB-REDO | |
|---|---|---|
| Crystallographic refinement | ||
| R | 0.1889 | 0.1885 |
| R-free |
0.2254
R-free was considered biased, the
estimated unbiased R-free was used
|
0.2232 |
| Bond length RMS Z-score | 0.811 | 0.413 |
| Bond angle RMS Z-score | 0.960 | 0.614 |
| Model quality | ||
| Ramachandran plot normality | -2.616 21 | -1.414 44 |
| Rotamer normality | -2.719 37 | -1.525 61 |
| Coarse packing | -0.320 34 | -0.038 47 |
| Fine packing | -1.413 35 | -1.127 48 |
| Bump severity | 0.009 59 | 0.005 72 |
| Hydrogen bond satisfaction | 0.871 22 | 0.879 28 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 12 |
| Side chains flipped | 0 |
| Waters removed | 10 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |