This entry is not up to date with the most recent version of PDB-REDO.
Please log in
to request an update.
Cholera toxin classical B-pentamer in complex with Lewis-y |
This entry was created with PDB-REDO version 8.04. |
From original header | |||||||
---|---|---|---|---|---|---|---|
Spacegroup | P 21 21 21 | a: 72.333 Å | b: 98.984 Å | c: 152.019 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
Resolution | 1.08 Å | Reflections | 369961 | Test set | 18334 (5.0%) | ||
R | 0.1205 | R-free | 0.1555 | ||||
According to PDB-REDO | |||||||
Resolution | 1.08 Å | Reflections | 369961 | Test set | 18334 (5.0%) | ||
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 | 0.1210 | 0.1293 |
R-free | 0.1556 | 0.1575 |
Bond length RMS Z-score | 1.870 | 0.881 |
Bond angle RMS Z-score | 1.209 | 0.934 |
Model quality | ||
Ramachandran plot normality | 0.322 88 | 0.667 92 |
Rotamer normality | 0.425 94 | 1.089 98 |
Coarse packing | N/A N/A | N/A N/A |
Fine packing | N/A N/A | N/A N/A |
Bump severity | 0.000 95 | 0.000 95 |
Hydrogen bond satisfaction | N/A N/A | N/A N/A |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 40 |
Side chains flipped | 0 |
Waters removed | 196 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 6 |
Residues fitting density worse | 58 |