[phenixbb] effect of solvent fraction on density modification/solvent flattening for a membrane protein

Pascal EGEA pascal at msg.ucsf.edu
Wed May 28 17:10:53 PDT 2008

Dear All,

This is a question about the effect of solvent fraction estimation on  
the quality of the initial phases.
I am trying to solve the structure of a membrane protein at moderate  
resolution 3.5A from a MAD data set (peak, inflection and high  
I have one copy of my complex which gives me a solvent fraction of  
0.7 without considering the contribution of the detergent.
With a related molecule I found a Phaser-MR solution but it does not  
refine although it is right.
I am using Phenix with the phases obtained from molecular replacement  
and combining them with the MAD signal to locate the seleniums. A  
visual inspection of the anomalous fourier difference map shows 6  
sites out of the 7 expected at 4sigma  contouring.

If I let Phenix decide by itself it goes on its own with  two copies  
in the ASU and considers a solvent fraction of 0.50; then it finds 7  
sites (and not 14 ? why is that?) (the seventh is weak but we expect  
this for this region of the complex).
now if I force Phenix to take ncs_copies=1 and solvent fraction=0.7  
then it only find 6 sites.

Wether it is 2 "freely chosen" molecules/ASU and 0.5 of solvent  or 1  
"forced" molecule/ASU and 0.7 of solvent, the 6 first sites are  
identical (although occupancies are quite higher in the first case)
Should I take into account the detergent and lower somewhat my  
solvent fraction (in the 0.6 range maybe) with the fixed one copy ASU  
estimation or just trust Solve/Resolve when it runs the density  
modification part. Does it really affect the quality of the phasing?  
Between these two extremes I am surprised to see that the quality of  
the resolve map are quite similar apparently showing clear new  
structural features.

Thanks in advance for your comments,

Pascal F. Egea, PhD
Post Doctoral Researcher
University of California San Francisco
Department of Biophysics and Biochemistry
Robert Stroud Laboratory
pascal at msg.ucsf.edu

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20080528/b5c5e943/attachment-0003.htm>

More information about the phenixbb mailing list