Crystal structure of Agrocybe cylindracea galectin with lactose |
This entry was created with PDB-REDO version 8.08. |
From original header | |||||||
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Spacegroup | P 61 | a: 125.368 Å | b: 125.368 Å | c: 56.589 Å | α: 90.00° | β: 90.00° | γ: 120.00° |
Resolution | 1.90 Å | Reflections | 39725 | Test set | 2034 (5.1%) | ||
R | 0.1733 | R-free | 0.1963 | ||||
According to PDB-REDO | |||||||
Resolution | 1.90 Å | Reflections | 39725 | Test set | 2034 (5.1%) | ||
Twin | false | Radiation damage | 63 | ||||
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 | 0.1779 | 0.1724 |
R-free | 0.1937 | 0.1905 |
Bond length RMS Z-score | 1.200 | 0.577 |
Bond angle RMS Z-score | 1.023 | 0.801 |
Model quality | ||
Ramachandran plot normality | -2.146 29 | -1.314 47 |
Rotamer normality | -3.278 28 | -2.172 47 |
Coarse packing | 2.148 98 | 2.262 98 |
Fine packing | 0.358 89 | 0.497 91 |
Bump severity | 0.014 47 | 0.011 54 |
Hydrogen bond satisfaction | 0.905 57 | 0.917 73 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 6 |
Side chains flipped | 0 |
Waters removed | 2 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 1 |
Residues fitting density worse | 0 |