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Figure 6
Problematic MR search models (green) and their r.m.s.d. values compared with the final structure (orange). (a) It was only possible to refine the Mtr3-Rrp42 solution when archaeal Rrp41-Rrp42 was used as the search model. The r.m.s.d. values are lower than those of the evolutionarily closer human Mtr3-Rrp42 model. (b) The N-terminal domains of Csl4 and Rrp40 were built manually. Despite their small size, their structural differences are remarkable. (c) Searching for the full-length Rrp44 was not possible. With an r.m.s.d. value of 9.20 Å, the conformational differences were large enough to hinder successful solution searches. Breaking the protein into two parts artificially decreases the r.m.s.d. values from 9.20 to 0.51 Å (PIN) and 2.04 Å (RNase II-like region). These two search models immediately yielded single solutions. All r.m.s.d. values were calculated using the `super' command in PyMOL v.1.3 (Schrödinger).

Journal logoBIOLOGICAL
ISSN: 1399-0047
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