TABLE 1.

Radius of gyration, global dimensions, and goodness of fit of the Turtle model of nHDL_DMPC with experimental SANS data

	Radius of Gyrationa (Å)		Dimensions (Å)	χ2ab
Model	Protein	Lipid	L × W × H	Proteina	Lipida
Experimental:c
nHDLDMPC	52.4	30.4	—	—	—
nHDLDMPC+Chol	50.7	33.5	—	—	—
SANS shapes:
nHDLDMPC	51.4	30.3	174 × 112 × 82	0.840d	2.291d
nHDLDMPC+Chol	50.8	35.4	114 × 113 × 56	0.880d	0.950d
EMe			173 × 105 × 51
Turtle model	52.0	30.2	175 × 103 × 62	0.985f 1.103g	2.309f 3.646g
Belt modelh	48.7	29.9	106 × 106 × 22i	5.436	7.458
1AV1j,k	48.9	—	126 × 89 × 52i	4.024	—
Saddle-1 modelk	48.9	—	104 × 104 × 48i	5.306	—
Saddle-2 modelk	46.4	—	101 × 92 × 58i	4.455	—
Saddle-3 modelk	44.9	—	91 × 91 × 63i	7.292	—
Saddle-4 modelk	41.4	—	80 × 80 × 73i	12.790	—

Radius of gyration (R_g) and overall dimensions of the low resolution structures (SANS shapes) and the Turtle, Belt, and Saddle models of nHDL_DMPC. Calculated χ² statistics (root mean square difference), that quantify differences between experimentally determined scattering intensities (measured by SANS with contrast variation) and theoretically calculated, show a better fit for the Turtle model compared with the Belt or various Saddle models of apoA1 dimer. EM, electron microscopy.

^aCalculated with CRYSON.

^bThe root mean square difference between the calculated and experimental scattering intensities.

^cCalculated with GNOM from experimental scattering intensity using the Guinier approximation.

^dCalculated with DAMMIN.

^eParticle dimensions of nHDL_DMPC from negative staining EM images (see Fig. 1).

^fA short energy minimization in vacuum was performed with GROMACS for each component (protein and lipid) individually (see Materials and Methods).

^gFull energy minimization in solution was performed with GROMACS for the nHDL_DMPC model (see Materials and Methods).

^hSupplementary Fig. VIII.

ⁱProtein component only.

^jThe crystal structure of lipid-free truncated (Δ43) apoA1 dimer.

^kSupplementary Figs. XII and XIII (15).