8W48

Neutron and X-ray joint structure of WT-TTR in complex with piceatannol

X-RAY DIFFRACTION - NEUTRON DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8W43

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	Disodium malonate, 0.1M NaOAc pH 4.6

Crystal Properties
Matthews coefficient	Solvent content
1.75	29.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.67	α = 90
b = 85.014	β = 90
c = 65.353	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	293	PIXEL	DECTRIS EIGER X 16M		2022-06-19	M	SINGLE WAVELENGTH
2	1	neutron	293	DIFFRACTOMETER	iBIX		2022-05-13	L	LAUE

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-17A	0.98	Photon Factory	BL-17A
2	SPALLATION SOURCE	J-PARC MLF BEAMLINE BL-03	2.8-5.7	JPARC MLF	BL-03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	R Split (All)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.19	42.51	99.8			0.04	0.016	0.999		23.8	6.3		78555
2	1.9	22.33	98.8			0.153	0.062	0.994		14.9	6.97		19613

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	R Split (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.19	1.23				0.876	0.352	0.774		2.3
2	1.9	1.97				0.646	0.315	0.556		2.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	1.19	42.507		1.36		78550	3927	99.77		0.1804	0.1793	0.2018
NEUTRON DIFFRACTION	MOLECULAR REPLACEMENT	1.9	21.784				19579	977	98.87		0.1797	0.1783	0.2064

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	19.121
f_dihedral_angle_d	19.121
f_angle_d	0.917
f_angle_d	0.917
f_chiral_restr	0.096
f_chiral_restr	0.096
f_bond_d	0.029
f_bond_d	0.029
f_plane_restr	0.005
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1771
Nucleic Acid Atoms
Solvent Atoms	102
Heterogen Atoms	36

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.