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Crystal structure of Agrocybe cylindracea galectin mutant (N46A) with blood type A antigen tetraose |
This entry was created with PDB-REDO version 8.04. |
From original header | |||||||
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Spacegroup | P 65 | a: 102.824 Å | b: 102.824 Å | c: 74.578 Å | α: 90.00° | β: 90.00° | γ: 120.00° |
Resolution | 1.60 Å | Reflections | 59060 | Test set | 2988 (5.1%) | ||
R | 0.1478 | R-free | 0.1749 | ||||
According to PDB-REDO | |||||||
Resolution | 1.60 Å | Reflections | 59060 | Test set | 2988 (5.1%) | ||
Twin | false | Radiation damage | N/A | ||||
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 | |
---|---|---|
Crystallographic refinement | ||
R | 0.1483 | 0.1383 |
R-free | 0.1730 | 0.1670 |
Bond length RMS Z-score | 0.789 | 0.595 |
Bond angle RMS Z-score | 0.694 | 0.713 |
Model quality | ||
Ramachandran plot normality | -0.062 79 | -0.036 79 |
Rotamer normality | 0.465 96 | 0.646 97 |
Coarse packing | 2.320 99 | 2.275 99 |
Fine packing | 0.038 83 | 0.174 85 |
Bump severity | 0.003 82 | 0.000 96 |
Hydrogen bond satisfaction | 0.915 71 | 0.921 78 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 9 |
Side chains flipped | 0 |
Waters removed | 14 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 1 |
Residues fitting density worse | 0 |