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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 | |||||||
|---|---|---|---|---|---|---|---|
| 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 |