Crystal structure of beta-glycosides-binding protein (W177X) of ABC transporter in a closed state bound to laminaritriose (Form I) |
This entry was created with PDB-REDO version 8.13 using the deposited PDB model version 1.3 |
From original header | |||||||
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Spacegroup | P 21 21 21 | a: 57.930 Å | b: 63.550 Å | c: 110.230 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
Resolution | 2.30 Å | Reflections | 18641 | Test set | 867 (4.7%) | ||
R | 0.2026 | R-free | 0.2649 | ||||
According to PDB-REDO | |||||||
Resolution | 2.30 Å | Reflections | 18641 | Test set | 867 (4.7%) | ||
Twin | false | Radiation damage | 85 | ||||
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 | 0.2047 | 0.2078 |
R-free | 0.2671 | 0.2620 |
Bond length RMS Z-score | 1.465 | 0.198 |
Bond angle RMS Z-score | 1.215 | 0.435 |
Model quality | ||
Ramachandran plot normality | -2.312 26 | -0.971 56 |
Rotamer normality | -3.437 26 | -1.081 70 |
Coarse packing | 1.014 85 | 1.067 86 |
Fine packing | -1.068 50 | -0.708 64 |
Bump severity | 0.009 59 | 0.005 72 |
Hydrogen bond satisfaction | 0.895 43 | 0.895 43 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 7 |
Side chains flipped | 0 |
Waters removed | 2 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 0 |
Residues fitting density worse | 0 |