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. 2009 Oct;15(10):1875–1885. doi: 10.1261/rna.1700409

FIGURE 4.

FIGURE 4.

Three models of the rat 28S rRNA loop E. The models are shown colored and the crystal structure in gray (PDB code 1Q9A). (Blue) Well modeled regions (RMSD < 0.5 Å), (red) badly modeled regions (RMSD > 3.0 Å). The models were optimally aligned (all atoms but H) with the crystal structure. (A) Model with a good INF (0.88; TP 29; FP 6; FN 2) and a good RMSD (1.64 Å); DI = 1.86. (B) Model with a good INF (0.88; TP 28; FP 5; FN 3), but a bad RMSD (3.76 Å); DI = 4.30. Although the geometry of the base pairs is well conserved, the thread through the phosphate atoms is shifted. (C) Model with a bad INF (0.71; TP 21; FP 7; FN 10), but a good RMSD (2.03 Å); DI = 2.85. The thread through the phosphate atoms is well superimposed, but the base-pairing geometry is wrong. Structural features that lead to a bad INF include: (D) base-stacking parameters that differ between the crystal (yellow) and model (blue) structures, such as G9, which shows a high rise in the crystal structure when compared with the model, and A19, for which a tilt can be observed between the crystal and model structures; and (E) base-pairing parameters that differ between the crystal and model structures, such as C20, which flips (propeller twist of 180°) between the crystal and model structures.