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| The crystal structure of the GH30 subfamily 10 enzyme, AcXbh30A from Acetivibrio clariflavus in complex with xylobiose |
| This entry was created with PDB-REDO version 8.04 using the deposited PDB model version 1.2 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 1 21 1 | a: 59.130 Å | b: 107.494 Å | c: 66.861 Å | α: 90.00° | β: 89.88° | γ: 90.00° |
| Resolution | 1.50 Å | Reflections | 124905 | Test set | 5961 (4.8%) | ||
| R | 0.1647 | R-free | 0.2136 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.50 Å | Reflections | 124905 | Test set | 5961 (4.8%) | ||
| Twin |
true
Data treated as twinned, but there may be other (symmetry) issues
|
Radiation damage | N/A | ||||
| 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 | 0.1646 | 0.1747 |
| R-free | 0.2082 | 0.1946 |
| Bond length RMS Z-score | 0.446 | 0.496 |
| Bond angle RMS Z-score | 0.627 | 0.660 |
| Model quality | ||
| Ramachandran plot normality | -1.925 31 | -1.478 41 |
| Rotamer normality | -0.873 80 | -0.372 88 |
| Coarse packing | 1.203 96 | 1.305 97 |
| Fine packing | -0.838 59 | -0.602 68 |
| Bump severity | 0.028 31 | 0.015 47 |
| Hydrogen bond satisfaction | 0.901 52 | 0.907 60 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 16 |
| Side chains built | 2 |
| Waters removed | 35 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |