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Crystal structure of a family 98 glycoside hydrolase catalytic module (Sp3GH98) in complex with the blood group A-trisaccharide (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: 92.270 Å | b: 153.750 Å | c: 96.880 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
Resolution | 1.45 Å | Reflections | 119761 | Test set | 6024 (5.0%) | ||
R | 0.1245 | R-free | 0.1590 | ||||
According to PDB-REDO | |||||||
Resolution | 1.45 Å | Reflections | 119761 | Test set | 6024 (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 | 0.1218 | 0.1439 |
R-free | 0.1562 | 0.1661 |
Bond length RMS Z-score | 1.051 | 0.515 |
Bond angle RMS Z-score | 0.904 | 0.823 |
Model quality | ||
Ramachandran plot normality | -0.233 77 | -0.252 76 |
Rotamer normality | 0.304 93 | 0.397 94 |
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 | 12 |
Side chains flipped | 7 |
Waters removed | 142 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 0 |
Residues fitting density worse | 6 |