Cholera toxin El Tor B-pentamer in complex with A-pentasaccharide |
This entry was created with PDB-REDO version 8.06. |
From original header | |||||||
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Spacegroup | P 21 21 21 | a: 63.626 Å | b: 84.720 Å | c: 84.720 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
Resolution | 1.55 Å | Reflections | 153564 | Test set | 7664 (5.0%) | ||
R | 0.1791 | R-free | 0.2196 | ||||
According to PDB-REDO | |||||||
Resolution | 1.55 Å | Reflections | 153564 | Test set | 7664 (5.0%) | ||
Twin | false | Radiation damage | 58 | ||||
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 | |
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Crystallographic refinement | ||
R | 0.1791 | 0.1811 |
R-free | 0.2197 | 0.2066 |
Bond length RMS Z-score | 1.374 | 0.611 |
Bond angle RMS Z-score | 1.004 | 0.685 |
Model quality | ||
Ramachandran plot normality | -0.427 72 | 0.504 90 |
Rotamer normality | -1.349 65 | -0.237 86 |
Coarse packing | 1.849 96 | 1.848 96 |
Fine packing | 0.030 83 | 0.260 87 |
Bump severity | 0.085 11 | 0.099 10 |
Hydrogen bond satisfaction | 0.887 35 | 0.891 39 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 27 |
Side chains flipped | 0 |
Waters removed | 87 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 1 |
Residues fitting density worse | 0 |