[phenixbb] refinement of partly occupied water molecules?

krimmer at staff.uni-marburg.de krimmer at staff.uni-marburg.de
Thu May 30 05:48:37 PDT 2013

Dear all,

I have a question concerning the refinement of partly occupied water  

in some of my macromolecular crystal structures with resolutions  
between 1.1 - 1.4 Å, mainly in the second solvation shell round  
positive Fo-Fc electron density blobs are detectable which show after  
assignment of a water molecule to these blob and subsequent refinement  
with Phenix refine a good-looking calculated 2Fo-Fc electron density  
(round shape, the 2Fo-Fc map appears at a contour level of σ = 1.0 -  
1.4), but there also occurs a small negative Fo-Fc electron density  
detectable inside the 2Fo-Fc density blob. The negative Fo-Fc electron  
density disappears if the occupancy of the water molecule is refined  
by Phenix or manually set lower than 100% occupancy. Therefore, I  
think these positions are partly occupied by water molecules, but I am  
not sure how I should handle it/how it is generally handled. I would  
be thankful for any advice and/or literature about this topic.

My second question is concerning a density blob in perfect  
coordination distance to an indolyl group (perfectly located in the  
middle of the five-ring, with 3.4 Å distance to every of the five  
carbon atoms of the five-ring). What‘s the best way to find out which  
ion possibly occupies this position? I tried Na+ and Ca2+, but after  
refinement big negative Fo-Fc blobs appear in both cases (maybe the  
ion at this position is only partly occupied?). There is no anomalous  
signal detectable at this position (data collection wavelength was  
0.91841 nm). After the refinement of a water molecule at this  
position, a positive Fo-Fc election density is still there.

Thank you for your help!


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