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. 2016 Jan 1;72(Pt 1):131–146. doi: 10.1107/S2059798315022111

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© Li et al. 2016

This is an open-access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.

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NCS-averaged OMIT maps of the Sm site superposed on the final coordinates of the Sm site. The OMIT maps (green) are calculated (§2.4) following molecular replacement, rigid-body refinement and restrained refinement by repeating the restrained refinement with the occupancies of the Sm-site nonanucleotide set to 0.01 and averaging the mF _o − DF _c density over the 12 NCS copies. (a) The U1-derived OMIT map contoured at 8.0σ (0.09 e Å⁻³) shows that at the G→U substitution U123 (marked by *) of U4 snRNA is bound in SmD₁. (b) The U4–U1 hybrid-derived OMIT map contoured at 7.5σ (0.08 e Å⁻³) shows that the first A of the U4 Sm-site nonamer, A118 (marked by *), is bound in SmF. Figs. 2–5 and 7–10 were prepared using PyMOL (v.1.7.2; Schrödinger).