5AKT
Transthyretin binding heterogeneity and anti-amyloidogenic activity of natural polyphenols and their metabolites: resveratrol-4'-O- glucuronide
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) |
Synchrotron site | PETRA III, EMBL c/o DESY |
Beamline | P13 (MX1) |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2013-08-31 |
Detector | DECTRIS PILATUS 6M |
Spacegroup name | P 21 21 2 |
Unit cell lengths | 42.741, 85.496, 63.672 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 63.672 - 1.350 |
R-factor | 0.1717 |
Rwork | 0.171 |
R-free | 0.19460 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 1f41 |
RMSD bond length | 0.011 |
RMSD bond angle | 1.518 |
Data reduction software | XDS |
Data scaling software | Aimless |
Phasing software | PHENIX |
Refinement software | PHENIX ((PHENIX.REFINE)) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 63.670 | 1.370 |
High resolution limit [Å] | 1.350 | 1.350 |
Rmerge | 0.030 | 0.530 |
Number of reflections | 51577 | |
<I/σ(I)> | 26.4 | 3.4 |
Completeness [%] | 99.3 | 99.1 |
Redundancy | 6.4 | 6.6 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | CRYSTALS OF WT HUMAN TTR- LIGAND COMPLEXES WERE OBTAINED AT ROOM TEMPERATURE IN ABOUT ONE WEEK BY CO-CRYSTALLIZATION, USING THE HANGING-DROP VAPOR DIFFUSION METHOD. THE PROTEIN (5 MG/ML), IN 20 MM SODIUM PHOSPHATE, PH 7, WAS INCUBATED WITH A FOUR-FOLD MOLAR EXCESS OF LIGANDS SOLUBILIZED IN DMSO. DROPS WERE FORMED BY MIXING EQUAL VOLUMES OF THE SOLUTION CONTAINING LIGAND-TTR COMPLEXES AND OF THE RESERVOIR/PRECIPITANT SOLUTION (2.2 M AMMONIUM SULPHATE, 0.1 M KCL, 0.03 M SODIUM PHOSPHATE, PH 7.0). |