This entry is not up to date with the most recent version of PDB-REDO.
Please log in
to request an update.
Crystal structure of alpha-1,3/4-fucosidase from Bifidobacterium longum subsp. infantis D172A/E217A mutant complexed with lacto-N-fucopentaose II |
This entry was created with PDB-REDO version 7.33. |
From original header | |||||||
---|---|---|---|---|---|---|---|
Spacegroup | P 21 21 21 | a: 82.588 Å | b: 105.971 Å | c: 120.715 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
Resolution | 2.10 Å | Reflections | 60159 | Test set | 3047 (5.1%) | ||
R | 0.1730 | R-free | 0.2230 | ||||
According to PDB-REDO | |||||||
Resolution | 2.10 Å | Reflections | 60159 | Test set | 3047 (5.1%) | ||
Twin | false | Radiation damage | N/A | ||||
PDB-REDO files | |||||||
Re-refined and rebuilt structure | Re-refined (only) structure |
All files
(compressed) |
|||||
Links | |||||||
PDBe | RCSB PDB | 3D bionotes | Proteopedia |
Original | PDB-REDO | |
---|---|---|
Crystallographic refinement | ||
R | 0.1744 | 0.1742 |
R-free | 0.2199 | 0.2003 |
Bond length RMS Z-score | 1.013 | 0.482 |
Bond angle RMS Z-score | 0.994 | 0.722 |
Model quality | ||
Ramachandran plot normality | -1.957 30 | -0.831 58 |
Rotamer normality | -2.688 45 | -1.157 74 |
Coarse packing | -0.591 32 | -0.503 36 |
Fine packing | -1.617 27 | -1.458 33 |
Bump severity | 0.034 26 | 0.045 21 |
Hydrogen bond satisfaction | 0.898 48 | 0.891 39 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 15 |
Side chains flipped | 0 |
Waters removed | 9 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 0 |
Residues fitting density worse | 0 |