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The crystal structure of the GH30 subfamily 10 enzyme, AcXbh30A from Acetivibrio clariflavus in complex with xylobiose |
This entry was created with PDB-REDO version 8.04 using the deposited PDB model version 1.2 |
From original header | |||||||
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Spacegroup | P 1 21 1 | a: 59.130 Å | b: 107.494 Å | c: 66.861 Å | α: 90.00° | β: 89.88° | γ: 90.00° |
Resolution | 1.50 Å | Reflections | 124905 | Test set | 5961 (4.8%) | ||
R | 0.1647 | R-free | 0.2136 | ||||
According to PDB-REDO | |||||||
Resolution | 1.50 Å | Reflections | 124905 | Test set | 5961 (4.8%) | ||
Twin |
true
|
Radiation damage | N/A | ||||
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 | 0.1646 | 0.1747 |
R-free | 0.2082 | 0.1946 |
Bond length RMS Z-score | 0.446 | 0.496 |
Bond angle RMS Z-score | 0.627 | 0.660 |
Model quality | ||
Ramachandran plot normality | -1.925 31 | -1.478 41 |
Rotamer normality | -0.873 80 | -0.372 88 |
Coarse packing | 1.203 96 | 1.305 97 |
Fine packing | -0.838 59 | -0.602 68 |
Bump severity | 0.028 31 | 0.015 47 |
Hydrogen bond satisfaction | 0.901 52 | 0.907 60 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 16 |
Side chains flipped | 2 |
Waters removed | 35 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 0 |
Residues fitting density worse | 0 |