4HJT

Kinetic stabilization of transthyretin through covalent modification of K15 by (E)-N-(4-(4-hydroxy-3,5-dimethylstyryl)phenyl)propionamide

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	298	THE WT-TTR WAS CONCENTRATED TO 4 MG/ML IN 10 MM NAPI, 100 MM KCL, AT PH 7.6 AND CO-CRYSTALLIZED AT ROOM TEMPERATURE WITH INHIBITORS USING THE VAPOR-DIFFUSION SITTING DROP METHOD, CRYSTALS WERE GROWN FROM 1.395 M SODIUM CITRATE, 3.5% V/V GLYCEROL AT PH 5.5. THE CRYSTALS WERE FROZEN USING A CRYO-PROTECTANT SOLUTION OF 1.395 M SODIUM CITRATE, PH 5.5, CONTAINING 10% V/V GLYCEROL, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.966	α = 90
b = 85.157	β = 90
c = 64.132	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		PIXEL	PSI PILATUS 6M	Rh coated flat mirror	2012-04-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.9795	SSRL	BL11-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	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	1.45	85.16	99.9	0.044	55.9	8.2		42818			20.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.45	1.5	100		0.519	3.7	8.1	4221

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2FBR	1.45	85.16	42350	2139	99.56	0.1665	0.1654	0.1873	RANDOM	23.2489

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]
0.6			-0.36		-0.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.154
r_dihedral_angle_4_deg	20.317
r_dihedral_angle_3_deg	14.591
r_scangle_it	7.076
r_dihedral_angle_1_deg	6.211
r_scbond_it	4.696
r_mcangle_it	3.596
r_mcbond_it	2.198
r_rigid_bond_restr	1.904
r_angle_refined_deg	1.727

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.154
r_dihedral_angle_4_deg	20.317
r_dihedral_angle_3_deg	14.591
r_scangle_it	7.076
r_dihedral_angle_1_deg	6.211
r_scbond_it	4.696
r_mcangle_it	3.596
r_mcbond_it	2.198
r_rigid_bond_restr	1.904
r_angle_refined_deg	1.727
r_angle_other_deg	0.954
r_mcbond_other	0.619
r_chiral_restr	0.109
r_bond_refined_d	0.017
r_gen_planes_refined	0.01
r_gen_planes_other	0.005
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1785
Nucleic Acid Atoms
Solvent Atoms	82
Heterogen Atoms	44

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction

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.