HNMMC refinement of the gRNA fragment 2394–2604 inside MS2. (A) The definition of DOFs of the gRNA fragment 2394–2604. The red fragment in Levels 1 and 2 of DOF 1 is the natural move that moves as a group. For Levels 3 and 4 of DOF 2, the different colors represent different natural moves. The black region at all levels is fixed. In Levels 3 and 4, the black region is the gRNA fragment 2468–2481 with a high-resolution EM structure. The gray color represents unpaired RNA loops that can also move. (B) The initial model of the gRNA fragment 2394–2604 and the corresponding cryo-EM density. The helical stems are colored as Level 3. (C) HNMMC refined model of the gRNA fragment 2394–2604 against the target cryo-EM density. The thin red line is the backbone trace from the previous published result (Dai et al. 2017).
