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| GH127 beta-L-arabinofuranosidase HypBA1 E322Q mutant complexed with p-nitrophenyl beta-L-arabinofuranoside |
| This entry was created with PDB-REDO version 8.06 using the deposited PDB model version 1.3 |
| From original header | |||||
|---|---|---|---|---|---|
| Spacegroup | P 32 2 1 | a: 78.182Å b: 78.182Å c: 78.182Å | α: 90.00° β: 90.00° γ: 120.00° | ||
| Resolution | 2.30 Å | Reflections | 40965 | Test set | 2114 (5.2%) |
| R | 0.2516 | R-free | 0.2898 | ||
| According to PDB-REDO | |||||
| Resolution | 2.30 Å | Reflections | 40965 | Test set | 2114 (5.2%) |
| Twin | false | Radiation damage | 8 | ||
| PDB-REDO files | |||||
| Re-refined and rebuilt structure |
Re-refined (only) structure
|
All files
(compressed) |
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| Links | |||||
| PDBe | RCSB PDB | Proteopedia | |||
| Original | PDB-REDO | |
|---|---|---|
| Crystallographic refinement | ||
| R | 0.2338 | 0.2082 |
| R-free | 0.2742 | 0.2488 |
| Bond length RMS Z-score | 1.452 | 0.458 |
| Bond angle RMS Z-score | 0.985 | 0.645 |
| Model quality | ||
| Ramachandran plot normality | -3.505 12 | -2.068 30 |
| Rotamer normality | -3.895 20 | -1.776 55 |
| Coarse packing | -0.078 45 | 0.100 53 |
| Fine packing | -1.284 41 | -0.992 53 |
| Bump severity | 0.014 47 | 0.012 51 |
| Hydrogen bond satisfaction | 0.847 13 | 0.853 15 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 6 |
| Side chains built | 0 |
| Waters removed | 0 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 12 |
| Residues fitting density worse | 0 |