This entry is not up to date with the most recent version of PDB-REDO.
Please log in
to request an update.
An active enzyme from the plant Viola yedoensis |
This entry was created with PDB-REDO version 8.04. |
From original header | |||||||
---|---|---|---|---|---|---|---|
Spacegroup | P 21 21 21 | a: 63.570 Å | b: 63.880 Å | c: 151.880 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
Resolution | 2.30 Å | Reflections | 28257 | Test set | 1352 (4.8%) | ||
R | 0.1748 | R-free | 0.2174 | ||||
According to PDB-REDO | |||||||
Resolution | 2.30 Å | Reflections | 28257 | Test set | 1352 (4.8%) | ||
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 | 0.1776 | 0.1691 |
R-free | 0.2147 | 0.2101 |
Bond length RMS Z-score | 0.539 | 0.505 |
Bond angle RMS Z-score | 0.808 | 0.669 |
Model quality | ||
Ramachandran plot normality | -0.131 77 | 0.012 80 |
Rotamer normality | -1.138 75 | -0.414 87 |
Coarse packing | 0.719 89 | 0.685 88 |
Fine packing | -1.986 15 | -1.906 17 |
Bump severity | 0.613 1 | 0.474 2 |
Hydrogen bond satisfaction | 0.862 18 | 0.873 23 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 12 |
Side chains flipped | 0 |
Waters removed | 33 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 0 |
Residues fitting density worse | 0 |