Experiment: 4PME

Human transthyretin (TTR) complexed with ferulic acid and curcumin.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4PM1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	protein: 5 mg/ml dialysed in 0.1 M NaCl, 0.05 M NaAc, pH 5.5 with 5 milli-M curcumin. precipitant:: 45% MPEG 2,000, 0.1 M sodium cacodylate, pH 7.5. Cryoprotectant: 40% mixed (25% dioxane, 25% DMSO, 12.5% ethylene glycol, 12.5% 1,2-propanediol, 12.5% glycerol, 12.5% 2,3-butanediol), 50% (25% MPEG 5000, 0.1 M mixed (Na acetate, ADA, Bicine buffer: 40% pH 4.0 / 60% pH 9.0)

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.99	α = 90
b = 84.67	β = 90
c = 64.06	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	100	PIXEL	DECTRIS PILATUS 6M	bent cylindrical mirror	2014-04-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.979338	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.26	42.335	99.7	0.055	0.052	18.58	8.84	63275	63061		-3	18.24

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.26	1.34	98.2		1.02	8.53

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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	THROUGHOUT	4PM1	1.264	42.335	1.36	63057	3153	99.68	0.1822	0.1809	0.183	0.2066	0.2061	Random

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	17.681
f_angle_d	1.178
f_chiral_restr	0.046
f_bond_d	0.007
f_plane_restr	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1803
Nucleic Acid Atoms
Solvent Atoms	278
Heterogen Atoms	60

Software

Software
Software Name	Purpose
PHENIX	refinement
REFMAC	refinement
XDS	data scaling
Coot	model building
ADSC	data collection