5AKV

Transthyretin binding heterogeneity and anti-amyloidogenic activity of natural polyphenols and their metabolites: genistein-7-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	42.843, 84.959, 63.636
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	63.636 - 1.520
R-factor	0.1717
Rwork	0.170
R-free	0.20040
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	1f41
RMSD bond length	0.011
RMSD bond angle	1.515
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]	63.640	1.550
High resolution limit [Å]	1.520	1.520
Rmerge	0.060	0.520
Number of reflections	36372
<I/σ(I)>	16.8	3
Completeness [%]	99.9	98.5
Redundancy	6.5	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).