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. Author manuscript; available in PMC: 2012 Nov 12.
Published in final edited form as: J Mol Biol. 2006 Feb 10;358(1):193–212. doi: 10.1016/j.jmb.2006.01.094

Figure 2.

Figure 2

Rigid-body refinement of the rRNA model. Fifty-two independent rigid units were defined for refinement of the RNA structure using Monte Carlo with simulated annealing (see methods). Regions are colored to represent the distinct units that were used for the refinement. Unmodeled regions are represented as dashed, grey lines. Helices 13, 50 and 59.1, proposed by comparative sequence analysis (http://rna.icmb.utexas.edu), did not fit the EM density. We propose an alternate structure in the region with helices 50 and 59.1 in domain III (see Figs. 3 and 4).