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Crystal structure of SdgB (complexed with UDP, GlcNAc, and Glycosylated peptide) |
This entry was created with PDB-REDO version 8.04. |
From original header | |||||||
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Spacegroup | P 21 21 21 | a: 70.201 Å | b: 130.568 Å | c: 189.854 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
Resolution | 2.50 Å | Reflections | 60648 | Test set | 3041 (5.0%) | ||
R | 0.1910 | R-free | 0.2400 | ||||
According to PDB-REDO | |||||||
Resolution | 2.45 Å | Reflections | 60648 | Test set | 3041 (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 | 0.1975 | 0.1952 |
R-free | 0.2431 | 0.2259 |
Bond length RMS Z-score | 1.380 | 0.238 |
Bond angle RMS Z-score | 1.056 | 0.456 |
Model quality | ||
Ramachandran plot normality | -2.079 28 | -0.915 56 |
Rotamer normality | -2.576 47 | -0.239 89 |
Coarse packing | 1.340 97 | 1.479 98 |
Fine packing | -0.834 59 | -0.443 72 |
Bump severity | 0.087 12 | 0.097 11 |
Hydrogen bond satisfaction | 0.888 36 | 0.888 36 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 20 |
Side chains flipped | 0 |
Waters removed | 0 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 6 |
Residues fitting density worse | 0 |