This entry is not up to date with the most recent version of PDB-REDO.
Please log in
to request an update.
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 |
This entry was created with PDB-REDO version 8.01. |
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 |
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 | 0.1779 | 0.1620 |
R-free | 0.2196 | 0.1980 |
Bond length RMS Z-score | 0.727 | 0.656 |
Bond angle RMS Z-score | 1.097 | 0.906 |
Model quality | ||
Ramachandran plot normality | -2.615 20 | -1.486 40 |
Rotamer normality | -3.107 38 | -1.639 65 |
Coarse packing | -0.090 57 | 0.007 62 |
Fine packing | -1.031 52 | -0.853 59 |
Bump severity | 0.021 38 | 0.020 39 |
Hydrogen bond satisfaction | 0.881 29 | 0.886 34 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 11 |
Side chains flipped | 0 |
Waters removed | 22 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 10 |
Residues fitting density worse | 0 |