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| Crystal structure of sugar binding protein CbpB complexed wtih laminaribiose from Clostridium thermocellum |
| This entry was created with PDB-REDO version 8.08 using the deposited PDB model version 1.2 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 1 21 1 | a: 72.750 Å | b: 46.440 Å | c: 116.490 Å | α: 90.00° | β: 106.58° | γ: 90.00° |
| Resolution | 1.68 Å | Reflections | 81514 | Test set | 1856 (2.3%) | ||
| R | 0.1734 | R-free | 0.2099 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.68 Å | Reflections | 81514 | Test set | 1856 (2.3%) | ||
| Twin | false | Radiation damage | 22 | ||||
| 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 | 0.1809 | 0.1783 |
| R-free | 0.2133 | 0.2131 |
| Bond length RMS Z-score | 0.573 | 0.308 |
| Bond angle RMS Z-score | 0.683 | 0.515 |
| Model quality | ||
| Ramachandran plot normality | -0.878 59 | -0.224 77 |
| Rotamer normality | -1.546 60 | -0.457 83 |
| Coarse packing | 1.721 95 | 1.861 96 |
| Fine packing | -1.880 17 | -1.600 28 |
| Bump severity | 0.001 90 | 0.003 81 |
| Hydrogen bond satisfaction | 0.903 54 | 0.911 65 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 6 |
| Side chains flipped | 7 |
| Waters removed | 91 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 4 |
| Residues fitting density worse | 0 |