Criteria for docking
We had four criteria for acceptable docking. (1) DBD-A and DBD-B both had to appear to make protein-DNA contacts that have been demonstrated biochemically. The first HTH makes stronger contacts with the DNA8 than the second HTH and had to sit properly in the major groove. As best as possible, the second HTH also needed to be over the major groove. (2) Each half-site had to be roughly centered on the appropriate DBD. (3) Using the surface representation feature in PyMol (https://pymol.org), the docked structures had to have good surface complementarity but could not intersect each other. (4) Because AraC has been shown experimentally to bind to direct-repeatI1-I2 ,6 we chose docked structures with the DBDs oriented as indicated in the biochemical contact experiments in which the second HTH is closer to RNA polymerase (see Discussion).