Cholera toxin El Tor B-pentamer in complex with Lewis-y |
This entry was created with PDB-REDO version 8.06. |
From original header | |||||||
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Spacegroup | P 1 21 1 | a: 63.667 Å | b: 80.916 Å | c: 80.916 Å | α: 90.00° | β: 96.07° | γ: 90.00° |
Resolution | 1.50 Å | Reflections | 146071 | Test set | 7329 (5.0%) | ||
R | 0.2214 | R-free | 0.2596 | ||||
According to PDB-REDO | |||||||
Resolution | 1.50 Å | Reflections | 146071 | Test set | 7329 (5.0%) | ||
Twin | false | Radiation damage | 27 | ||||
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 | 0.2192 | 0.2200 |
R-free | 0.2570 | 0.2461 |
Bond length RMS Z-score | 1.334 | 0.655 |
Bond angle RMS Z-score | 1.057 | 0.698 |
Model quality | ||
Ramachandran plot normality | -0.913 58 | 0.908 94 |
Rotamer normality | -1.965 51 | -0.219 87 |
Coarse packing | 1.869 96 | 1.917 97 |
Fine packing | 0.031 83 | 0.331 88 |
Bump severity | 0.075 12 | 0.071 13 |
Hydrogen bond satisfaction | 0.868 21 | 0.880 29 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 33 |
Side chains flipped | 0 |
Waters removed | 10 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 1 |
Residues fitting density worse | 0 |