4PVN

Neutron structure of human transthyretin (TTR) at room temperature to 2.3A resolution (monochromatic)

NEUTRON DIFFRACTION - X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.4	293	2.15M SODIUM MALONATE, 23MG/ML PROTEIN, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.68	α = 90
b = 86.26	β = 90
c = 65.72	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	neutron	293	AREA DETECTOR	HE3 POSITION SENSITIVE DETECTOR		2010-06-23	M	SINGLE WAVELENGTH
2	1	x-ray	293	CCD	ADSC QUANTUM 315r		2011-02-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	NUCLEAR REACTOR	OTHER	2.42
2	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.9791	ESRF	ID23-1

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	2.3	52.276	99.3	0.152						7.7	3.5	11438	11395	1.3	1.3	14.9
2	1.85	43.13	99.4	0.093						7.4	3.5		21718		2	19.8

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	2.3	2.42		0.645						1.6	2.6	1613
2	1.85	1.95		0.42						2.67	3.49

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
NEUTRON DIFFRACTION		2.3	52.276		1.35		11395	571	98.62		0.2118	0.2093	0.262
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	1.95	43.13		1.34		18655	933	99.44		0.1574	0.156	0.1851		29.56

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]
-1.804			2.1028		-0.2988
-0.2524			-0.1038		0.3562

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	15.627
f_angle_d	1.309
f_chiral_restr	0.084
f_bond_d	0.012
f_plane_restr	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1801
Nucleic Acid Atoms
Solvent Atoms	84
Heterogen Atoms

Software

Software
Software Name	Purpose
MADSYS	phasing
PHENIX	model building
PHENIX	refinement
RETREAT	data reduction
SCALA	data scaling
PHENIX	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.