You've probably done it already, but solvent flattening/flipping/massaging at 80% solvent should provide a cheap thrill with regard to phase improvement.
=====================================
Phoebe A. Rice
Dept. of Biochemistry & Molecular Biology
The University of Chicago
phone 773 834 1723
http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123
http://www.rsc.org/shop/books/2008/9780854042722.asp
---- Original message ----
>Date: Fri, 28 Jan 2011 14:29:07 -0600
>From: CCP4 bulletin board <[log in to unmask]> (on behalf of Todd Geders <[log in to unmask]>)
>Subject: [ccp4bb] Noisy difference maps with high solvent content?
>To: [log in to unmask]
>
> Greetings CCP4bb,
>
> Short version:
>
> Very noisy difference maps from a crystal with
> extremely high solvent content, seeking advice on
> how best to handle such high solvent content to
> eliminate noise in difference maps.
> http://strayxray.com/images/coot.jpg
>
> Long version:
>
> I'm having trouble with a 3.0Å dataset from a
> crystal with 80% solvent content. The space group
> is P4132 and I'm quite confident the high solvent
> content is real (there is a species-specific set of
> helices extending into the solvent channels that
> appears to prevent tighter packing).
>
> I was able to get a MR solution using a structurally
> related enzyme, but the difference maps are terribly
> noisy (see link). There are lots of negative
> density in empty spaces between well-defined 2Fo-Fc
> electron density.
>
> http://strayxray.com/images/coot.jpg
>
> The 2Fo-Fc density actually looks fairly good. The
> initial MR maps had clear density correlating to the
> sequence differences between the MR model and the
> crystallized protein. After fixing the model as
> best I could, the refinement statistics are R/Rfree
> of 27.5/30.3 with a data/parameters ratio of 1.7.
>
> The mosaicity ranges from 0.15-0.3, data were
> collected with 0.5° oscillations and 180° of data
> were collected.
>
> http://strayxray.com/images/diffraction.jpg
>
> Since the crystals appeared to suffer from radiation
> decay (based on scaling statistics), I only use the
> first 40° of data (which still gives around 8-fold
> redundancy). Using more minimal wedges of data or
> more data does not noticeably make better or noisier
> maps.
>
> Any advice on improving the maps? Could the noisy
> maps be due to the extraordinarily high solvent
> content?
>
> I'd appreciate any advice or comments.
>
> ~Todd Geders
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