| Crystallographic structure of oligosaccharide dehydrogenase from Pycnoporus cinnabarinus bound to Guaiacol, orthorhombic crystal |
| This entry was created with PDB-REDO version 8.17 using the deposited PDB model version 1.0 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 21 21 21 | a: 48.891 Å | b: 61.530 Å | c: 195.206 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
| Resolution | 1.78 Å | Reflections | 92185 | Test set | 4541 (4.9%) | ||
| R | 0.1675 | R-free | 0.2186 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.29 Å | Reflections | 92185 | Test set | 4541 (4.9%) | ||
| Twin | false | Radiation damage | 0 | ||||
| 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 | 0.3325 | 0.2143 |
| R-free | 0.3566 | 0.2524 |
| Bond length RMS Z-score | 1.756 | 0.481 |
| Bond angle RMS Z-score | 1.346 | 0.700 |
| Model quality | ||
| Ramachandran plot normality | -1.599 40 | -1.599 40 |
| Rotamer normality | -2.318 44 | -1.867 53 |
| Coarse packing | 0.373 65 | 0.403 67 |
| Fine packing | -1.376 37 | -1.435 35 |
| MolProbity Clashscore | 10.380 23 | 6.850 39 |
| Hydrogen bond satisfaction | 0.870 22 | 0.873 24 |
| WHAT_CHECK | Report | No Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | N/A |
| Side chains built | 0 |
| Waters removed | N/A |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 8 |
| Residues fitting density worse | 0 |