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Crystal structure of the catalytic module of a family 98 glycoside hydrolase from Streptococcus pneumoniae SP3-BS71 in complex with the A-trisaccharide blood group antigen. |
This entry was created with PDB-REDO version 7.32. |
From original header | |||||||
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Spacegroup | P 21 21 2 | a: 97.720 Å | b: 153.800 Å | c: 91.040 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
Resolution | 1.90 Å | Reflections | 104893 | Test set | 5245 (5.0%) | ||
R | 0.1650 | R-free | 0.2060 | ||||
According to PDB-REDO | |||||||
Resolution | 1.90 Å | Reflections | 104893 | Test set | 5245 (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 | 0.1625 | 0.1604 |
R-free | 0.2007 | 0.1879 |
Bond length RMS Z-score | 0.785 | 0.391 |
Bond angle RMS Z-score | 0.775 | 0.651 |
Model quality | ||
Ramachandran plot normality | -1.073 51 | -0.615 64 |
Rotamer normality | -1.093 76 | -0.079 91 |
Coarse packing | -0.156 54 | -0.155 54 |
Fine packing | -1.914 17 | -1.743 22 |
Bump severity | 0.011 56 | 0.003 82 |
Hydrogen bond satisfaction | 0.895 44 | 0.903 54 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 38 |
Side chains flipped | 0 |
Waters removed | 12 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 1 |
Residues fitting density worse | 0 |