[phenixbb] problem refining RNA structure at 4Å resolution

Francis Reyes Francis.Reyes at colorado.edu
Wed May 29 07:10:48 PDT 2013

You are likely suffering from model bias towards your search model and low data:parameter ratio in your refinement. 

How many molecules per asu?

How different is the search model vs the target? At this resolution keep in mind that you won't be able to tell much, such as the effect of a single nucleotide substitution or indel unless it results in large changes in the structure. 


On May 29, 2013, at 5:53 AM, Benoît Masquida <b.masquida at ibmc-cnrs.unistra.fr> wrote:

> Dear phenix users,
> I solved using MR a low resolution RNA structure taking data up to 4.3Å and a model of a structure with slight differences. However, when I try to refine, Rwork decreases quickly (start 47, final 32 but Rfree remains high (start 48, final 44). The data are pretty good up to 4.0 with I/sigma above 1. The map doesn't point clearly to wrong regions of the model. What can I try to improve the maps and build the correct model?
> Thanks in advance.
> Benoit
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