Extended Data Fig. 4. Assignment of bases to the syn conformation.
a, Nucleotide G4, which forms the long-range base pair with C76 in the pseudoknot, is in a syn conformation. Top: Placement of the base into an anti conformation results in positive and negative density (green and red, respectively) in the Fo-Fc map (left, contoured at 3σ), and the 2Fo-Fc map (right) shows the base is incorrectly placed (blue density, contoured at 1.5 σ). In contrast, placement of the base into the syn conformation (bottom) results in a flat Fo-Fc map (left, contoured at 3σ) and a good fit to the 2 Fo-Fc map (right, blue density contoured at 1.5 σ). Base A11 is also in a syn conformation; the same analysis was performed to verify this (not shown). b, 2Fo-Fc map surrounding bases A3-C4. The G4′s C4′-C5′ bond is best modeled in the trans conformation.