Crystal structure of the UcaD lectin-binding domain in complex with fucose |
This entry was created with PDB-REDO version 8.08. |
From original header | |||||||
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Spacegroup | I 4 | a: 79.472 Å | b: 79.472 Å | c: 70.227 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
Resolution | 1.50 Å | Reflections | 34586 | Test set | 1999 (5.8%) | ||
R | 0.1626 | R-free | 0.1761 | ||||
According to PDB-REDO | |||||||
Resolution | 1.50 Å | Reflections | 34586 | Test set | 1999 (5.8%) | ||
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 | 0.1680 | 0.1424 |
R-free | 0.1786 | 0.1655 |
Bond length RMS Z-score | 0.675 | 0.844 |
Bond angle RMS Z-score | 0.698 | 0.755 |
Model quality | ||
Ramachandran plot normality | -0.988 56 | -1.113 52 |
Rotamer normality | 1.185 98 | 1.217 98 |
Coarse packing | -0.628 22 | -0.674 21 |
Fine packing | -1.379 37 | -1.214 44 |
Bump severity | 0.002 85 | 0.000 95 |
Hydrogen bond satisfaction | 0.920 77 | 0.923 80 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 4 |
Side chains flipped | 0 |
Waters removed | 28 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 12 |
Residues fitting density worse | 0 |