. Author manuscript; available in PMC: 2014 Sep 3.

Published in final edited form as: Structure. 2004 Sep;12(9):1607–1618. doi: 10.1016/j.str.2004.06.019

Table 3. Results Obtained by Fitting Crystallographic Structural Components into the Mature and Immature Dengue Virus Maps.

					Molecule 1^d			Molecule 2^d			Molecule 3^d

	Model	Sumf^a	Clash^b	–Den^c	DI^e	DII^e	DIII^e	DI^e	DII^e	DIII^e	DI^e	DII^e	DIII^e
Mature	DEN sE(H) with β-OG	38.2	0.7	2.4	36.5	39.0	36.0	38.8	39.4	37.4	38.9	39.2	36.5
	DEN sE(H) without β-OG	38.6	0.4	1.9	36.8	39.7	36.0	39.3	40.3	37.3	39.1	39.7	36.3
	DEN sE(P)	37.3	1.1	3.0	36.6	37.2	35.8	38.7	37.6	36.8	38.8	37.5	36.1
	DEN sE(P) DI + DIII and DII^f	39.3	1.6	1.3	36.9	40.7	36.3	39.4	41.5	38.1	39.2	40.8	37.0
Immature	DEN sE(H) with β-OG	46.1	3.1	2.5	43.8	52.0	41.4	41.9	51.3	39.5	42.5	52.7	40.8
	DEN sE(H) without β-OG	46.6	2.3	1.8	45.0	52.6	40.9	43.2	50.9	40.4	44.0	51.9	41.8
	DEN sE(P)	47.0	2.1	1.5	45.3	52.9	41.0	43.4	52.3	39.8	44.4	53.3	40.6
	DEN sE(P) DI + DIII and DII^f	47.5	0.1	1.3	46.5	52.4	43.3	44.7	51.4	42.7	43.3	51.7	42.3

Sumf is defined as the average value of density at all atomic positions normalized by setting the highest density in the map to 100. The higher Sumf values for the immature virus density are probably primarily the result of the extensive contact of the E and prM proteins, thus placing the atoms of E in the contact area into higher density. This is particularly true for DII.

Clash represents the percentage of atoms in the model that have steric clashes with symmetry-related subunits.

–Den denotes the percentage of atoms that are positioned in negative density.

Molecules 1, 2, and 3 are nonicosahedral symmetry-related molecules as shown in Figures 4 and 5.

Sumf values for domains DI, DII, and DIII, respectively.

Two rigid bodies, DI + DIII and DII, were fitted independently using both icosahedral and nonicosahedral symmetry as described in the Experimental Procedures section.