| 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 8.20 using the deposited PDB model version 3.2 |
| From original header | |||||
|---|---|---|---|---|---|
| Spacegroup | P 21 21 21 | a: 68.566Å b: 101.602Å c: 103.696Å | 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 | 61 | ||
| PDB-REDO files | |||||
| Re-refined and rebuilt structure |
Re-refined (only) structure
|
All files
(compressed) |
|||
| Links | |||||
| PDBe | RCSB PDB | Proteopedia | |||
| Original | PDB-REDO | |
|---|---|---|
| Crystallographic refinement | ||
| R | 0.1885 | 0.1918 |
| R-free |
0.2249
R-free was considered biased, the
estimated unbiased R-free was used
|
0.2305 |
| Bond length RMS Z-score | 0.811 | 0.227 |
| Bond angle RMS Z-score | 0.960 | 0.464 |
| Model quality | ||
| Ramachandran plot normality | -2.616 21 | -1.788 35 |
| Rotamer normality | -2.719 37 | -1.153 69 |
| Coarse packing | -0.320 34 | -0.157 42 |
| Fine packing | -1.413 35 | -1.210 44 |
| MolProbity Clashscore | 3.830 65 | 2.020 87 |
| Hydrogen bond satisfaction | 0.874 24 | 0.868 21 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | N/A |
| Side chains built | 0 |
| Waters removed | N/A |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |