Figure 5. Movements in the surface helices of cytochrome b in the presence of stigmatellin. The brown net is the electron density calculated from a native crystal (no inhibitors) and the red model is the backbone of cytochrome b built into this density. The blue net is density from a crystal containing stigmatellin. The purple backbone and connected side chains are the Rieske protein located in this density, and the other ball-and-stick models are depict stigmatellin and parts of cytochrome b. Both electron density maps are made using experimental phases after improvement by density modification, and are contoured at 1 s . The models are unrefined and intended only to identify features of the density. It can be seen that the cd1 helix moves down, perhaps pushed by the Rieske protein in docking, and the ef helix and residue Y279 move to the right, perhaps as expansion of the Qo site to accommodate stigmatellin. Rieske H161 which H-bonds stigmatellin is deep in the picture; the electron density can be seen dimmed by the depth-cueing. The descending arm of the ef linker with P271 and E272 is not seen because it is in front of the slab of space used for the picture. Artifacts due to differences in cell parameters and different positioning of the protein in the two cells was avoided by transforming the models and skewing the maps to a reference cell in sucha a way as to optimally superimpose the rest of the protein.