Dear all,
I have a question concerning the refinement of partly occupied water
molecules:
in some of my macromolecular crystal structures with resolutions
between 1.1 - 1.4 Å, several round positive Fo-Fc electron density
blobs are detectable which show after assignment of a water molecule
to these blobs and subsequent refinement with Phenix.refine a
good-looking 2Fo-Fc electron density. However, 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 automatically refined by
Phenix.refine (occupancy manually set to a value below 100% followed
by refinement) or manually set to 50% and fixed for this value (Fix
occupancy option in phenix.refine). 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. Which one of the two options
described above is the better one? I would be thankful for any advice
and/or literature about this topic.
Thank you for your help!
Stefan
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