Crystal structure of GH36 alpha-galactosidase AgaA A355E D478A from Geobacillus stearothermophilus in complex with stachyose |
This entry was created with PDB-REDO version 8.06. |
From original header | |||||||
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Spacegroup | P 32 2 1 | a: 154.070 Å | b: 154.070 Å | c: 154.070 Å | α: 90.00° | β: 90.00° | γ: 120.00° |
Resolution | 3.60 Å | Reflections | 38121 | Test set | 1906 (5.0%) | ||
R | 0.2377 | R-free | 0.2822 | ||||
According to PDB-REDO | |||||||
Resolution | 3.60 Å | Reflections | 38121 | Test set | 1906 (5.0%) | ||
Twin | false | Radiation damage | N/A | ||||
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 | 0.2576 | 0.1959 |
R-free | 0.2959 | 0.2408 |
Bond length RMS Z-score | 0.481 | 0.726 |
Bond angle RMS Z-score | 0.538 | 0.842 |
Model quality | ||
Ramachandran plot normality | -2.528 23 | -3.884 10 |
Rotamer normality | -3.422 26 | -4.889 10 |
Coarse packing | -0.476 28 | -0.116 43 |
Fine packing | -2.466 6 | -1.856 18 |
Bump severity | 0.089 11 | 0.074 13 |
Hydrogen bond satisfaction | 0.790 5 | 0.806 6 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 11 |
Side chains flipped | 0 |
Waters removed | 0 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 115 |
Residues fitting density worse | 0 |