5NFE

Neutron structure of human transthyretin (TTR) T119M mutant at room temperature to 1.85A resolution

X-RAY DIFFRACTION - NEUTRON DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	1.9M sodium malonate pD5.9, 40mg/ml protein

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.71	α = 90
b = 86.32	β = 90
c = 65.338	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	298	IMAGE PLATE	BIODIFF		2016-09-08	M	SINGLE WAVELENGTH
2	1	x-ray	293	PIXEL	DECTRIS PILATUS 6M-F		2016-10-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	NUCLEAR REACTOR	FRM II BEAMLINE BIODIFF	2.67	FRM II	BIODIFF
2	SYNCHROTRON	ESRF BEAMLINE ID30B	0.9763	ESRF	ID30B

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	1.85	43.61	90.6	0.164			0.136			3.7	2		19760
2	1.85	33.49	97.3	0.047			0.025			27.1	4.4		19760

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	1.85	1.9		0.526			0.499			1.2	1.7
2	1.85	1.95		0.062			0.033			16.7	4.3

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	1.853	43.16		1.99		20896	2091	96.34		0.1677	0.1648	0.1941
NEUTRON DIFFRACTION	MOLECULAR REPLACEMENT	1.85	33.485				19744	1975	90.69		0.2173	0.2132	0.2536

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	13.337
f_dihedral_angle_d	13.337
f_angle_d	1.548
f_angle_d	1.548
f_chiral_restr	0.082
f_chiral_restr	0.082
f_bond_d	0.014
f_bond_d	0.014
f_plane_restr	0.009
f_plane_restr	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1794
Nucleic Acid Atoms
Solvent Atoms	38
Heterogen Atoms

Software

Software
Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
XDS	data reduction
HKL-2000	data scaling
SCALA	data scaling
Coot	model building
REFMAC	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.