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. Author manuscript; available in PMC: 2013 Feb 8.
Published in final edited form as: J Am Chem Soc. 2012 Jan 27;134(5):2644–2652. doi: 10.1021/ja2093647

Figure 3.

Figure 3

Models of the pRNA 3-wj derived based on DEER distances measured in pRNA dimer. (A) Best-fit model obtained from grid search using the RMSDdeer criterion. HT, HL, and HR are shown in green, red, and blue, respectively. Angles between the respective helical axes are shown in the inset. To demonstrate that the best-fit model does satisfy the connection constraint, connections between HT/HR (U29), HR/HL (U72U73U74), and HT/HL (no nucleotide present) were manually built-in using conformations observed in the pRNA tetramer crystal structure43 (pdb no. 3R4F) with slight adjustment of backbone torsion angles. (B) Interhelical angle distributions from the 3662 viable models obtained using the RMSDdeer criterion. (C) Best-fit model obtained from grid search using the Rmsdmod criterion. The interhelical angles between HT/HL, HT/HR, and HR/HL are 90°, 46°, and 134°, respectively. (D) Best-fit model obtained from random docking search.