| 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 | |||||||
|---|---|---|---|---|---|---|---|
| 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 | |
|---|---|---|
| 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 |