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Crystal structure of a family 98 glycoside hydrolase catalytic module (Sp3GH98) in complex with the type 2 blood group A- tetrasaccharide (E558A X02 mutant) |
This entry was created with PDB-REDO version 8.04. |
From original header | |||||||
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Spacegroup | C 2 2 21 | a: 92.330 Å | b: 155.020 Å | c: 97.260 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
Resolution | 1.77 Å | Reflections | 67320 | Test set | 3399 (5.0%) | ||
R | 0.1626 | R-free | 0.2011 | ||||
According to PDB-REDO | |||||||
Resolution | 1.77 Å | Reflections | 67320 | Test set | 3399 (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 | |
---|---|---|
Crystallographic refinement | ||
R | 0.1562 | 0.1477 |
R-free | 0.1922 | 0.1849 |
Bond length RMS Z-score | 1.107 | 0.604 |
Bond angle RMS Z-score | 0.890 | 0.860 |
Model quality | ||
Ramachandran plot normality | -0.720 63 | -0.718 63 |
Rotamer normality | -0.370 84 | 0.064 90 |
Coarse packing | N/A N/A | N/A N/A |
Fine packing | N/A N/A | N/A N/A |
Bump severity | 0.000 95 | 0.000 95 |
Hydrogen bond satisfaction | N/A N/A | N/A N/A |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 13 |
Side chains flipped | 6 |
Waters removed | 33 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 2 |
Residues fitting density worse | 0 |