Experiment: 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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	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	0.1802	0.2018	0.2011
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

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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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.