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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 | |||||||
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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 |