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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, X01 mutant) |
This entry was created with PDB-REDO version 7.31. |
From PDB header | |||||||
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Spacegroup | C 2 2 21 | a: 92.160 Å | b: 154.780 Å | c: 97.260 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
Resolution | 2.03 Å | Reflections | 44001 | Test set | 2224 (5.1%) | ||
R | 0.1670 | R-free | 0.2150 | ||||
According to PDB-REDO | |||||||
Resolution | 2.03 Å | Reflections | 44001 | Test set | 2224 (5.1%) | Twin | false |
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 |
PDB | PDB-REDO | |
---|---|---|
Crystallographic refinement | ||
R | 0.1666 | 0.1559 |
R-free | 0.2090 | 0.1995 |
Bond length RMS Z-score | 0.469 | 0.386 |
Bond angle RMS Z-score | 0.603 | 0.646 |
Model quality | ||
Ramachandran plot normality | 1.007 53 | 0.998 53 |
Rotamer normality | 1.311 72 | 0.732 82 |
Coarse packing | 0.114 56 | 0.198 51 |
Fine packing | 2.094 12 | 1.962 15 |
Bump severity | 0.002 87 | 0.002 87 |
Hydrogen bond satisfaction | 0.886 34 | 0.895 44 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 21 |
Side chains flipped | 5 |
Waters removed | 10 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 0 |
Residues fitting density worse | 0 |