Hi Bert,
try phenix.refine: it uses very efficient and robust bulk solvent
correction and anisotropic scaling protocol (Acta Cryst. (2005). D61,
850-855) as well as it automatically detects and removes
reflections-outliers before the refinement starts. I think the
combination of these things may help.
More information:
http://phenix-online.org/
http://phenix-online.org/documentation/
http://phenix-online.org/documentation/refinement.htm
or replay me with your questions.
Cheers,
Pavel.
On 1/24/2008 3:21 PM, Van Den Berg, Bert wrote:
Hi all,
during refinement of our (membrane protein) structures, basically in
all cases the R/Rfree values depend a lot on the low resolution
cutoff. Putting the cutoff at lower res (20-50 A) results in
substantially higher R/Rfree values (sometimes few percent). For this
reason we mostly refine the data from the high-res limit down to 10A
or so. I have noticed that this occurs fairly often in the literature,
but I don't know if this is a membrane protein related issue or not.
Could it be that the bulk solvent model used in CNS (we refine
exclusively with CNS) does not model the situation with membrane
proteins, due to the presence of detergents? Or is it related to data
collection issues (low-res spots overloaded etc)? Anything else? What
could be done to overcome the problem, and to use all the data in
refinement?
Thanks, Bert
Bert van den Berg
University of Massachusetts Medical School
Program in Molecular Medicine
Biotech II, 373 Plantation Street, Suite 115
