This entry is not up to date with the most recent version of PDB-REDO.
Please log in
to request an update.
Crystal structure of the catalytic module of a family 98 glycoside hydrolase from Streptococcus pneumoniae TIGR4 in complex with the H- disaccharide blood group antigen. |
This entry was created with PDB-REDO version 7.32. |
From original header | |||||||
---|---|---|---|---|---|---|---|
Spacegroup | P 21 21 21 | a: 50.796 Å | b: 90.816 Å | c: 116.545 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
Resolution | 1.70 Å | Reflections | 58609 | Test set | 2961 (5.1%) | ||
R | 0.1430 | R-free | 0.1970 | ||||
According to PDB-REDO | |||||||
Resolution | 1.70 Å | Reflections | 58609 | Test set | 2961 (5.1%) | ||
Twin | false | Radiation damage | N/A | ||||
PDB-REDO files | |||||||
Re-refined and rebuilt structure | Re-refined (only) structure |
All files
(compressed) |
|||||
Links | |||||||
PDBe | RCSB PDB | 3D bionotes | Proteopedia |
Original | PDB-REDO | |
---|---|---|
Crystallographic refinement | ||
R | 0.1431 | 0.1527 |
R-free | 0.1963 | 0.1899 |
Bond length RMS Z-score | 0.655 | 0.511 |
Bond angle RMS Z-score | 0.762 | 0.742 |
Model quality | ||
Ramachandran plot normality | -0.765 60 | -0.601 65 |
Rotamer normality | -0.777 81 | -0.353 88 |
Coarse packing | 0.312 76 | 0.254 74 |
Fine packing | -2.012 14 | -2.055 13 |
Bump severity | 0.002 87 | 0.001 92 |
Hydrogen bond satisfaction | 0.892 40 | 0.899 49 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 15 |
Side chains flipped | 2 |
Waters removed | 13 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 0 |
Residues fitting density worse | 0 |