Hi Katja,
What I personally do in such a situation is to start to fill the density
by water oxygen atoms, refine a bit (the position plus the isotropic
temperature factors) and then compute a new map. Usually it has cleared
up somewhat, thus allowing you to find out what it really is. This is
what happened to me recently with a whole stretch of polypeptide that
was in a different position in the MR search model and in the structure.
After introducing water molecules, refinement and a new map, bingo: the
whole stretch could be modelled.
And PEG tails can be disordered too.
Fred.
Katja Schleider wrote:
Dear all,
I found some fairly substantial density in the active site of my
protein structure. But I don´t know what it should be. My
crystallisation condition consists of lithium sulfate,
citrate-phosphate and peg1000. The whole lot doesn't make a dashed bit
of sense! Any suggestions to fill this density with something?
Picture is attached.
Thanks a lot,
Katja
