| Ligand complex structure of GH10 family xylanase XynAF1, soaking for 120 minutes |
| This entry was created with PDB-REDO version 8.12 using the deposited PDB model version 2.1 |
| From original 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 | 0.1215 | R-free | 0.1507 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.50 Å | Reflections | 83792 | Test set | 4184 (5.0%) | ||
| Twin | false | Radiation damage |
100
Data shows severe radiation damage
|
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| 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 | 0.1222 | 0.1193 |
| R-free | 0.1518 | 0.1430 |
| Bond length RMS Z-score | 2.018 | 0.877 |
| Bond angle RMS Z-score | 1.473 | 0.895 |
| Model quality | ||
| Ramachandran plot normality | -1.122 52 | -0.760 62 |
| Rotamer normality | -0.406 84 | 0.057 90 |
| Coarse packing | 1.537 94 | 1.571 94 |
| Fine packing | 1.217 96 | 1.218 96 |
| Bump severity | 0.145 7 | 0.141 7 |
| Hydrogen bond satisfaction | 0.857 16 | 0.861 18 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 8 |
| Side chains flipped | 0 |
| Waters removed | 18 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |