A crystal structure of a 108 nucleotide RNA-DNA complex containing a four-way junction was solved at 3.1 Å resolution. The structure of the junction differs substantially from the "stacked-X' conformation observed previously due to a 135º rotation of the branches. Comparison of the two conformers provides insight into the factors contributing to the flexibility of four-way junctions. The stacked-X conformation maximizes base-stacking but causes unfavorable repulsion between phosphate groups, whereas the 135º -rotated "crossed" conformation minimizes electrostatic clashes at the expense of reduced base-stacking. Despite the large rotation of the branches, both junction structures exhibit an antiparallel arrangement of the continuous strands and opposite polarity of the crossover strands.