Crystal structure of GH36 alpha-galactosidase AgaA A355E D548N from Geobacillus stearothermophilus in complex with raffinose |
This entry was created with PDB-REDO version 8.06. |
From original header | |||||||
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Spacegroup | P 32 2 1 | a: 149.680 Å | b: 149.680 Å | c: 149.680 Å | α: 90.00° | β: 90.00° | γ: 120.00° |
Resolution | 2.60 Å | Reflections | 92575 | Test set | 4629 (5.0%) | ||
R | 0.1696 | R-free | 0.2212 | ||||
According to PDB-REDO | |||||||
Resolution | 2.60 Å | Reflections | 92575 | Test set | 4629 (5.0%) | ||
Twin | false | Radiation damage | 85 | ||||
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 | |
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Crystallographic refinement | ||
R | 0.1800 | 0.1648 |
R-free | 0.2244 | 0.1997 |
Bond length RMS Z-score | 0.473 | 0.490 |
Bond angle RMS Z-score | 0.538 | 0.633 |
Model quality | ||
Ramachandran plot normality | -1.842 34 | -1.151 51 |
Rotamer normality | -0.903 74 | -1.072 71 |
Coarse packing | 0.305 63 | 0.405 67 |
Fine packing | -0.975 54 | -0.795 61 |
Bump severity | 0.050 18 | 0.033 25 |
Hydrogen bond satisfaction | 0.872 23 | 0.882 30 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 36 |
Side chains flipped | 0 |
Waters removed | 70 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 5 |
Residues fitting density worse | 0 |