Crystal structure of beta-glycosides-binding protein (W177X) of ABC transporter in a closed state bound to laminaritriose (Form II) |
This entry was created with PDB-REDO version 8.06. |
From original header | |||||||
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Spacegroup | P 31 2 1 | a: 185.410 Å | b: 185.410 Å | c: 185.410 Å | α: 90.00° | β: 90.00° | γ: 120.00° |
Resolution | 2.80 Å | Reflections | 36300 | Test set | 1703 (4.7%) | ||
R | 0.1866 | R-free | 0.2356 | ||||
According to PDB-REDO | |||||||
Resolution | 2.80 Å | Reflections | 36300 | Test set | 1703 (4.7%) | ||
Twin | false | Radiation damage | 78 | ||||
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 | 0.1875 | 0.1820 |
R-free | 0.2369 | 0.2227 |
Bond length RMS Z-score | 1.469 | 0.626 |
Bond angle RMS Z-score | 1.160 | 0.754 |
Model quality | ||
Ramachandran plot normality | -2.473 23 | -1.527 41 |
Rotamer normality | -3.971 19 | -3.079 31 |
Coarse packing | 0.875 82 | 1.013 85 |
Fine packing | -1.384 37 | -1.056 51 |
Bump severity | 0.015 45 | 0.016 43 |
Hydrogen bond satisfaction | 0.868 21 | 0.868 21 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 12 |
Side chains flipped | 0 |
Waters removed | 0 |
Peptides flipped | 1 |
Chiralities fixed | 0 |
Residues fitting density better | 1 |
Residues fitting density worse | 0 |