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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 X01 mutant) |
This entry was created with PDB-REDO version 8.04. |
From original header | |||||||
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Spacegroup | C 2 2 21 | a: 92.240 Å | b: 154.670 Å | c: 96.770 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
Resolution | 1.98 Å | Reflections | 46645 | Test set | 2346 (5.0%) | ||
R | 0.1611 | R-free | 0.2060 | ||||
According to PDB-REDO | |||||||
Resolution | 1.98 Å | Reflections | 46645 | Test set | 2346 (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 | 0.1599 | 0.1501 |
R-free | 0.1977 | 0.1883 |
Bond length RMS Z-score | 1.027 | 0.371 |
Bond angle RMS Z-score | 0.860 | 0.701 |
Model quality | ||
Ramachandran plot normality | -0.727 63 | -0.735 63 |
Rotamer normality | -0.824 76 | -0.276 86 |
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 | 14 |
Side chains flipped | 5 |
Waters removed | 9 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 1 |
Residues fitting density worse | 0 |