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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-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 2.5 |
| 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 | Radiation damage | N/A | ||||
| 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 | 0.1786 | 0.1626 |
| R-free | 0.2197 | 0.1987 |
| Bond length RMS Z-score | 1.422 | 0.384 |
| Bond angle RMS Z-score | 1.086 | 0.599 |
| Model quality | ||
| Ramachandran plot normality | -2.664 21 | -1.469 43 |
| Rotamer normality | -3.132 30 | -1.232 67 |
| Coarse packing | -0.090 45 | 0.009 49 |
| Fine packing | -1.031 52 | -0.909 57 |
| Bump severity | 0.021 36 | 0.016 43 |
| Hydrogen bond satisfaction | 0.878 27 | 0.888 36 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 8 |
| Side chains flipped | 0 |
| Waters removed | 25 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 14 |
| Residues fitting density worse | 0 |