Cholera toxin classical B-pentamer in complex with Lewis-x |
This entry was created with PDB-REDO version 8.06. |
From original header | |||||||
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Spacegroup | P 21 21 21 | a: 82.965 Å | b: 108.291 Å | c: 108.291 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
Resolution | 1.54 Å | Reflections | 153804 | Test set | 7676 (5.0%) | ||
R | 0.1926 | R-free | 0.2236 | ||||
According to PDB-REDO | |||||||
Resolution | 1.54 Å | Reflections | 153804 | Test set | 7676 (5.0%) | ||
Twin | false | Radiation damage | 79 | ||||
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 | 0.1921 | 0.1940 |
R-free | 0.2221 | 0.2145 |
Bond length RMS Z-score | 1.347 | 0.599 |
Bond angle RMS Z-score | 0.978 | 0.671 |
Model quality | ||
Ramachandran plot normality | -0.435 71 | 0.868 94 |
Rotamer normality | -1.215 68 | 0.029 90 |
Coarse packing | 1.663 95 | 1.668 95 |
Fine packing | 0.170 86 | 0.402 89 |
Bump severity | 0.030 27 | 0.025 32 |
Hydrogen bond satisfaction | 0.886 34 | 0.886 34 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 5 |
Side chains flipped | 0 |
Waters removed | 0 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 4 |
Residues fitting density worse | 0 |