Figure 5. Overall architecture of DEBS3.

Ten independent rigid body refinement models were generated for DEBS3 using CORAL with P2 symmetry applied and dimerization enforced across the KS and TE domains. The results were clustered using all-atom RMSD alignments under the default settings in DAMCLUST. (A) Cluster I includes 4/10 models (RMSD = 23 ± 4 Å), and cluster II includes 3/10 models (RMSD = 27 ± 4 Å). One representative from each cluster is shown. Domains are colored as in Figure 2B. (B) Theoretical scattering curves for structures in each cluster were fit to SAXS data using CRYSOL. The best agreement between theoretical and experimental scatterings curves was observed in the low-q region (q < 0.125), suggesting a resolution accuracy of ∼50 Å (d = 2π/q). Chi²-free values are reported in Table S4. (C) In order to assess the most accurate placement of M6 with respect to M5, we generated a library of conformers by rotating M6 from cluster I about the 2-fold axis of symmetry while keeping the position of M5 fixed. Each structure was fit to the experimental data, and the reported χ-values were plotted as a function of rotation angle. (D) P2 symmetry was applied during 10 independent ab initio calculations of the DEBS3 molecular envelope using DAMMIN. The models were binned into clusters based on lowest NSD between structures, using the default settings in DAMCLUST. Good agreement with rigid body models was observed for 7 of 10 structures. The average envelope from these structures was refined over 20 ab initio modeling cycles using DAMMIN. The filtered, average molecular envelope is shown in three orientations. All structures are scaled equivalently with a 100 Å scale bar provided in (A). (E) A schematic representation of DEBS3 shows we can place M6 colinear to M5. M6 may be rotated with respect to M5 by as much as 70° relative to the xy-plane of M5.