Bacterial beta-1,3-oligosaccharide phosphorylase from GH149 with laminarihexaose bound at a surface site |
This entry was created with PDB-REDO version 8.06. |
From original header | |||||||
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Spacegroup | P 21 21 21 | a: 99.129 Å | b: 158.756 Å | c: 158.756 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
Resolution | 2.25 Å | Reflections | 134106 | Test set | 6752 (5.0%) | ||
R | 0.1798 | R-free | 0.2173 | ||||
According to PDB-REDO | |||||||
Resolution | 2.25 Å | Reflections | 134106 | Test set | 6752 (5.0%) | ||
Twin | false | Radiation damage | 52 | ||||
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 | |
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Crystallographic refinement | ||
R | 0.1821 | 0.1776 |
R-free | 0.2199 | 0.2140 |
Bond length RMS Z-score | 0.847 | 0.369 |
Bond angle RMS Z-score | 0.738 | 0.550 |
Model quality | ||
Ramachandran plot normality | -1.389 45 | -1.193 50 |
Rotamer normality | -2.286 45 | -1.400 63 |
Coarse packing | 1.205 89 | 1.616 94 |
Fine packing | -1.430 35 | -0.948 55 |
Bump severity | 0.004 76 | 0.010 56 |
Hydrogen bond satisfaction | 0.914 69 | 0.905 57 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 66 |
Side chains flipped | 107 |
Waters removed | 88 |
Peptides flipped | 3 |
Chiralities fixed | 0 |
Residues fitting density better | 39 |
Residues fitting density worse | 2 |