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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-2-yl)-2-oxo-1,2-dihydropyridin-3-yl)carbamate (alpha-ketoamide 13b) |
| This entry was created with PDB-REDO version 8.08 using the deposited PDB model version 3.0 |
| 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 | N/A | ||||
| 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 | 0.1885 | 0.1880 |
| R-free |
0.2249
R-free was considered biased, the
estimated unbiased R-free was used
|
0.2228 |
| Bond length RMS Z-score | 0.810 | 0.415 |
| Bond angle RMS Z-score | 0.958 | 0.616 |
| Model quality | ||
| Ramachandran plot normality | -2.616 21 | -1.392 45 |
| Rotamer normality | -2.719 37 | -1.333 65 |
| Coarse packing | -0.320 34 | -0.041 47 |
| Fine packing | -1.910 17 | -1.568 29 |
| Bump severity | 0.009 59 | 0.008 62 |
| Hydrogen bond satisfaction | 0.878 27 | 0.880 29 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 17 |
| Side chains flipped | 0 |
| Waters removed | 9 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 1 |