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CCP4BB  January 2008

CCP4BB January 2008

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Subject:

Re: low-res cutoff in refinement

From:

Dale Tronrud <[log in to unmask]>

Reply-To:

Dale Tronrud <[log in to unmask]>

Date:

Thu, 24 Jan 2008 16:06:19 -0800

Content-Type:

text/plain

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text/plain (57 lines)

Dear Bert,

    I think is it important here to remember that R and R free are tools
to help judge the quality of the model, not the data.  You cannot reject
data because it disagrees with your model.  Lowering your free R by
changing your resolution limit is no different than finding all the
individual reflections that disagree most with your model and rejecting
them.  Neither procedure increasing the quality of your model, it
simply lowers the R value.

    If you suspect you have a problem with overloads, you have to go
to your data reduction log files and see if you have this problem.  If
you suspect your bulk solvent model is poor you need to find out what
model you are using and decide if it is correct for your crystal.  It
is certainly a good idea, as Pavel suggests in another response, to
try other programs that have different approaches.

    Membrane protein crystals have a particular problem with bulk solvent
because there is the lipid part of the bulk solvent and the water part
and most bulk solvent models assume a single kind of bulk solvent.
Hopefully someone else will reply with some references to such
two-component bulk solvent models.

    If you can't figure out how to lower your R's by improving your
model, I'm afraid you just have to live with it.  Your R values will
be higher because they reflect the inability of your model to fit
your data.

Dale Tronrud


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
> 
> 

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