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| Ligand complex structure of GH10 family xylanase XynAF1, soaking for 120 minutes |
| This entry was created with PDB-REDO version 7.32. |
| From PDB header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 1 | a: 44.330 Å | b: 57.106 Å | c: 64.734 Å | α: 74.19° | β: 80.96° | γ: 68.87° |
| Resolution | 1.50 Å | Reflections | 83792 | Test set | 4184 (5.0%) | ||
| R | 0.1220 | R-free | 0.1510 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.50 Å | Reflections | 83792 | Test set | 4184 (5.0%) | Twin | false |
| 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 | ||||
| PDB | PDB-REDO | |
|---|---|---|
| Crystallographic refinement | ||
| R | 0.1221 | 0.1236 |
| R-free | 0.1509 | 0.1468 |
| Bond length RMS Z-score | 1.183 | 0.647 |
| Bond angle RMS Z-score | 1.183 | 0.816 |
| Model quality | ||
| Ramachandran plot normality | 1.185 48 | 0.720 61 |
| Rotamer normality | 0.366 88 | 0.112 93 |
| Coarse packing | 0.288 75 | 0.338 77 |
| Fine packing | 0.384 89 | 0.552 91 |
| Bump severity | 0.175 6 | 0.186 6 |
| Hydrogen bond satisfaction | 0.872 23 | 0.876 25 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 7 |
| Side chains flipped | 0 |
| Waters removed | 16 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |