Crystal structure of the UcaD lectin-binding domain in complex with galactose |
This entry was created with PDB-REDO version 8.08. |
From original header | |||||||
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Spacegroup | I 4 | a: 79.360 Å | b: 79.360 Å | c: 70.360 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
Resolution | 1.72 Å | Reflections | 23065 | Test set | 1153 (5.0%) | ||
R | 0.1726 | R-free | 0.2028 | ||||
According to PDB-REDO | |||||||
Resolution | 1.72 Å | Reflections | 23065 | Test set | 1153 (5.0%) | ||
Twin | false | Radiation damage | 100 Data shows severe radiation damage | ||||
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 | 0.1781 | 0.1773 |
R-free | 0.2077 | 0.2096 |
Bond length RMS Z-score | 0.670 | 0.376 |
Bond angle RMS Z-score | 0.727 | 0.560 |
Model quality | ||
Ramachandran plot normality | -1.196 50 | -1.099 53 |
Rotamer normality | 0.400 94 | 0.420 94 |
Coarse packing | -0.630 22 | -0.627 22 |
Fine packing | -1.473 33 | -1.366 37 |
Bump severity | 0.001 90 | 0.001 90 |
Hydrogen bond satisfaction | 0.919 76 | 0.920 77 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 3 |
Side chains flipped | 0 |
Waters removed | 13 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 1 |
Residues fitting density worse | 0 |