Dear Marco,
in terms of using XDS, STRONG_PIXEL=99 is _highly_ non-standard (I
personally try to stick with the defaults ... although at synchrotrons I
do use STRONG_PIXEL=6 instead of the default of 3). I realize this is
just a way to pick the strong reflection for indexing (since
STRONG_PIXEL is used by COLSPOT , but not by INTEGRATE), but in the long
run it would be important to figure out the relation between the strong
lattice and the weak lattice (you could post the cell parameters here,
or even better upload a few frames to some Internet service so that
people can take a look themselves).
You seem to be able to solve the structure using the lattice
corresponding to the strong spots, if I understand correctly. The
lattice that covers both the weak and the strong spots certainly has
longer cell axes, and I'd guess that there are maybe twice as many
molecules in the ASU. Taking account of this, you may be able to solve
the structure using all reflections, and you might get some important
insight concerning the binding mode(s) of the substrate.
best,
Kay
Am 20:59, schrieb Marco Lolicato:
> Dear all,
> I have a particular problem...
> so, I have a beautiful crystal with nice diffraction pattern at 2.7A. The diffraction images are composed by very strong spots and weak spots.
> With XDS, if I collect all spots I get good map, but it is impossible to solve the structure by molecular replacement. If I collect only the strongest spots (STRONG_PIXEL=9), I'm able to solve a very good structure...
> My problem is: I was trying to get the apo-structure of my protein. I obtained nice crystals of the "apo-protein", but using the method above, in the structure I have found also the ligand!! (probably incorporated during the overexpression).
> My protein is a multimer and, biochemically, I found that the endogenus ligand bond to the protein is in the ratio 1:6. ...and I got a crystal in this way.
>
> So, is there a way to analyze all spots in the diffraction pattern to have a structure of the apo-protein?
> Is a good idea discard the strongest spots and try to analyze only the weak spots? If yes, how I can do it?
>
> All the best,
>
>
> Marco
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