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Crystal structure of a family 98 glycoside hydrolase catalytic module (Sp3GH98) in complex with the type 1 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: 92.260 Å | b: 154.750 Å | c: 97.160 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
Resolution | 1.65 Å | Reflections | 83477 | Test set | 4167 (5.0%) | ||
R | 0.1454 | R-free | 0.1856 | ||||
According to PDB-REDO | |||||||
Resolution | 1.65 Å | Reflections | 83477 | Test set | 4167 (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 | 0.1415 | 0.1523 |
R-free | 0.1805 | 0.1751 |
Bond length RMS Z-score | 1.053 | 0.542 |
Bond angle RMS Z-score | 0.891 | 0.818 |
Model quality | ||
Ramachandran plot normality | -0.503 69 | -0.509 69 |
Rotamer normality | 0.133 91 | 0.174 92 |
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 | 9 |
Side chains flipped | 5 |
Waters removed | 39 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 7 |
Residues fitting density worse | 1 |