Crystal structure of beta-glycosides-binding protein (W177X) of ABC transporter in an open-liganded state bound to laminaribiose |
This entry was created with PDB-REDO version 8.06. |
From original header | |||||||
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Spacegroup | P 1 21 1 | a: 62.510 Å | b: 92.250 Å | c: 92.250 Å | α: 90.00° | β: 112.42° | γ: 90.00° |
Resolution | 1.85 Å | Reflections | 62433 | Test set | 3076 (4.9%) | ||
R | 0.1682 | R-free | 0.2167 | ||||
According to PDB-REDO | |||||||
Resolution | 1.85 Å | Reflections | 62433 | Test set | 3076 (4.9%) | ||
Twin | false | Radiation damage | 58 | ||||
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 | 0.1688 | 0.1785 |
R-free | 0.2165 | 0.2108 |
Bond length RMS Z-score | 1.507 | 0.203 |
Bond angle RMS Z-score | 1.127 | 0.414 |
Model quality | ||
Ramachandran plot normality | -1.129 52 | -0.254 76 |
Rotamer normality | -2.305 45 | -0.478 82 |
Coarse packing | 1.305 91 | 1.210 89 |
Fine packing | -1.343 38 | -1.240 43 |
Bump severity | 0.006 68 | 0.003 81 |
Hydrogen bond satisfaction | 0.915 70 | 0.912 66 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 3 |
Side chains flipped | 0 |
Waters removed | 11 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 0 |
Residues fitting density worse | 0 |