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Crystal structure of glycoside hydrolase family 11 beta-xylanase from Streptomyces olivaceoviridis E-86 in complex with 4-O-methyl-alpha-D-glucuronopyranosyl xylotetraose |
This entry was created with PDB-REDO version 7.34. |
From PDB header | |||||||
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Spacegroup | P 32 | a: 142.709 Å | b: 142.709 Å | c: 72.454 Å | α: 90.00° | β: 90.00° | γ: 120.00° |
Resolution | 2.00 Å | Reflections | 110646 | Test set | 5434 (4.9%) | ||
R | 0.1650 | R-free | 0.2180 | ||||
According to PDB-REDO | |||||||
Resolution | 2.00 Å | Reflections | 110646 | Test set | 5434 (4.9%) | 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 |
PDB | PDB-REDO | |
---|---|---|
Crystallographic refinement | ||
R | 0.1659 | 0.1618 |
R-free | 0.2185 | 0.2021 |
Bond length RMS Z-score | 0.664 | 0.667 |
Bond angle RMS Z-score | 1.025 | 0.817 |
Model quality | ||
Ramachandran plot normality | 1.449 41 | 0.738 61 |
Rotamer normality | 1.934 59 | 0.267 89 |
Coarse packing | 0.026 63 | 0.136 69 |
Fine packing | 0.161 85 | 0.458 90 |
Bump severity | 0.062 16 | 0.037 24 |
Hydrogen bond satisfaction | 0.921 78 | 0.920 77 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 54 |
Side chains flipped | 0 |
Waters removed | 29 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 2 |
Residues fitting density worse | 0 |