This entry is not up to date with the most recent version of PDB-REDO.
Please log in
to request an update.
Ligand complex structure of GH10 family xylanase XynAF1, soaking for 120 minutes |
This entry was created with PDB-REDO version 7.32. |
From PDB header | |||||||
---|---|---|---|---|---|---|---|
Spacegroup | P 1 | a: 44.330 Å | b: 57.106 Å | c: 64.734 Å | α: 74.19° | β: 80.96° | γ: 68.87° |
Resolution | 1.50 Å | Reflections | 83792 | Test set | 4184 (5.0%) | ||
R | 0.1220 | R-free | 0.1510 | ||||
According to PDB-REDO | |||||||
Resolution | 1.50 Å | Reflections | 83792 | Test set | 4184 (5.0%) | Twin | false |
PDB-REDO files | |||||||
Re-refined and rebuilt structure | Re-refined (only) structure |
All files
(compressed) |
|||||
Links | |||||||
PDBe | RCSB PDB | 3D bionotes | Proteopedia |
PDB | PDB-REDO | |
---|---|---|
Crystallographic refinement | ||
R | 0.1221 | 0.1236 |
R-free | 0.1509 | 0.1468 |
Bond length RMS Z-score | 1.183 | 0.647 |
Bond angle RMS Z-score | 1.183 | 0.816 |
Model quality | ||
Ramachandran plot normality | 1.185 48 | 0.720 61 |
Rotamer normality | 0.366 88 | 0.112 93 |
Coarse packing | 0.288 75 | 0.338 77 |
Fine packing | 0.384 89 | 0.552 91 |
Bump severity | 0.175 6 | 0.186 6 |
Hydrogen bond satisfaction | 0.872 23 | 0.876 25 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 7 |
Side chains flipped | 0 |
Waters removed | 16 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 0 |
Residues fitting density worse | 0 |