Table 1. Fit of TBEV E Dimers onto an Icosahedral 2-Fold Axis of the CryoEM Dengue Map.

(A) Using the TBEV Dimer as Determined Crystallographically
Fit	Sumf	Clash	–Den	Theta 1	Cent (x, y, z)	D1, D2, D3
down+	53.0	0.0	29.0	24.5	0.0, 0.0, 232.5	48.6, 56.5, 49.4
down−	49.6	0.0	40.0	133.8	0.0, 0.0, 230.5	41.0, 52.1, 55.9
up+	44.8	0.0	82.0	119.8	0.0, 0.0, 233.5	38.1, 48.9, 59.9
up−	40.2	0.0	116.0	30.8	0.0, 0.0, 229.5	43.3, 36.7, 43.1
(B) Using the Dimer Found in Alphaviruses
down+	32.0	0.0	196.0	170.2	0.0, 0.0, 234.5	42.9, 23.2, 34.6
down−	31.4	0.0	159.0	103.2	0.0, 0.0, 231.0	38.1, 25.7, 27.7
up+	20.0	0.0	236.0	105.2	0.0, 0.0, 225.5	26.7, 11.6, 31.0
up−	32.0	0.0	201.0	81.0	0.0, 0.0, 234.0	55.8,37.1, −4.7
(C) Exploring the Pixel Size of the Dengue CryoEM Map by Fitting the TBEV E Dimer in the Preferred Down+ Manner
Pixel (Å)	Sumf	Clash	–Den	Theta 1	Cent (x, y, z)	D1, D2, D3
2.7	50.0	0.0	47.0	29.0	0.0, 0.0, 216.5	50.0, 54.6, 34.7
2.8	51.5	0.0	40.0	27.2	0.0, 0.0, 224.0	50.3, 55.3, 41.9
2.9	53.0	0.0	29.0	24.5	0.0, 0.0, 232.5	48.6, 56.5, 49.4
3.0	47.6	0.0	62.0	25.5	0.0, 0.0, 236.5	49.6, 47.1, 47.8
3.1	17.9	0.0	224.0	118.5	0.0, 0.0, 220.0	17.1, 8.7, 36.8

Sumf is the mean density height averaged over all atoms where the maximum density is scaled to have a value of 100; clash is the number of atoms in one molecule that approach closer than 6 A to another, symmetry-related molecule; –den are the number of atoms in negative density; theta 1 is the angle of rotation about the 2-fold axis; cent (x, y, z) is the position in the map onto which is placed the center of gravity of the TBEV E dimer (see Figure 1 for the definition of the coordinate system); D1, D2, D3 are the sumf values (the average atom density relative to the highest density of 100.0 in the map) for each of the three domains; down and up refer to the orientation of the dimer axis along the icosahedral axis; + and − refer to the assumed hand of the cryoEM map. The best fit is shown in each case.