TABLE 2.

Fitting of the E glycoprotein X-ray structure into the cryo-EM map^a

Moleculeb	sumf1c (%)	sumf2c (%)	sumf3c (%)	−dend (%)	clashe (%)	centxf (Å)	centyf (Å)	centzf (Å)
Green	50.6	59.0	51.2	0.0	0.2	33.1	−84.5	201.5
Red	48.5	56.4	49.3	0.0	0.0	92.2	−46.6	196.5
Blue	54.3	57.6	50.6	0.2	0.0	33.2	−4.4	220.5

^aThe Cα backbone of the West Nile virus E molecule (Protein Data Bank accession number, 2HG0) was used to fit into the NOIP and ACIP electron density maps with a procedure described by Zhang et al. (19) and Rossmann et al. (15). The pixel size of the ACIP and NOIP West Nile virus maps was adjusted with respect to the cryo-EM map of immature dengue virus by minimizing the root mean square difference in density within the external protein layer (between 190 and 290 Å radius). The cryo-EM densities on the two magnification-adjusted maps were then put onto the same relative scale by minimizing the function ∑(ρ_den − aρ_WN − b)² by using density values within the external protein region, where a and b are scale factors and ρ_den and ρ_WN are the density values for the dengue and West Nile virus immature particles, respectively. After having established both the magnification and density scale factors, the difference map between the dengue and West Nile virus immature particles was computed.

^bMolecule refers to the green, red, and blue color coding in Fig. 1 and 2E and F.

^csumf1, sumf2, and sumf3 are the average densities at Cα atoms for domains I, II, and III, respectively, expressed as percentages of the highest density in the map.

^d−den is the percentage of atoms in negative density.

^eclash is the percentage of atoms that sterically interfere between neighboring molecules.

^fcentx, centy, and centz are the coordinates of the center of mass of the E monomer in the map.