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| Crystal structure of glycoside hydrolase family 11 beta-xylanase from Streptomyces olivaceoviridis E-86 in complex with 4-O-methyl- alpha-D-glucuronopyranosyl xylotetraose |
| This entry was created with PDB-REDO version 8.04 using the deposited PDB model version 1.3 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 32 | a: 142.709 Å | b: 142.709 Å | c: 72.454 Å | α: 90.00° | β: 90.00° | γ: 120.00° |
| Resolution | 2.00 Å | Reflections | 110646 | Test set | 5434 (4.9%) | ||
| R | 0.1651 | R-free | 0.2176 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.00 Å | Reflections | 110646 | Test set | 5434 (4.9%) | ||
| Twin | false | 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 | 0.1655 | 0.1734 |
| R-free | 0.2181 | 0.2011 |
| Bond length RMS Z-score | 3.251 | 0.539 |
| Bond angle RMS Z-score | 0.983 | 0.651 |
| Model quality | ||
| Ramachandran plot normality | -1.358 43 | -0.746 60 |
| Rotamer normality | -1.934 59 | -0.462 86 |
| Coarse packing | 0.141 69 | 0.272 75 |
| Fine packing | 0.074 84 | 0.452 90 |
| Bump severity | 0.062 16 | 0.036 25 |
| Hydrogen bond satisfaction | 0.922 79 | 0.914 70 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 59 |
| Side chains flipped | 0 |
| Waters removed | 7 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 2 |