[sharp-discuss] Re: Heavy Atom Negative Density

[Paul Hubbard]

Thanks for the reply,

I had thought about that, especially with the Hg derivative. However, that anomlous signal, weak as it is, proves that the FeS cluster is still there. Also, the Hg crystal is still the same colour as before soaking; though, the Os crystal is black (even after a long de-soak).

By the way, I had originally made the mistake of omitting the FeS atoms in the derivatives in the first place, and still get negative density!!!

Paul Hubbard

Frank Vondelft wrote:

> Hi Paul
>
> Any chance that you lost the iron-sulfur during the soaking?  I don't know enough about the thing's biology, but what you see is what might happen if the derivatives do not have the cluster.  You could try defining the cluster only for the "native" (Fe MAD), not for the derivatives.  I assume you have set the right scattering factors for the Fe in the derivative datasets?
>
> (I've not been following this thread, sorry if this has been suggested before.)
>
> phx.
>
> > -----Original Message-----
> > From: Paul Hubbard [mailto:phubbard@post.its.mcw.edu]
> > Sent: Monday, February 04, 2002 8:26 AM
> > To: Clemens Vonrhein; sharp; ccp4
> > Subject: Re: [sharp-discuss] Re: Heavy Atom Negative Density
> >
> >
> > Hello,
> >
> > In followup to my previous e-mail, I have run both Fe MAD
> > data alone, and in
> > combination with the Os and Hg derivatives in SHARP. The MAD
> > data alone gives
> > nice positive denisty at the FeS cluster, but I still get
> > negative density when
> > I add the 2 derivatives (including the FeS atoms).
> >
> > NOTE: I know the Os and Hg derivatives are useable since SAS
> > phaing using native
> > in-house data with PHASES, and then doing X-Fouriers shows
> > really nice peaks in
> > the Fo-Fc maps, and this is confirmed using  Fe-MAD phases, and in the
> > isomorphous difference Patterson. I also triple checked using
> > SOLVE - so I'm
> > pretty sure its right.
> >
> > However, when I run the data through RESOLVE I get, what
> > looks like on first
> > impressions (though I could be very wrong), a traceable map -
> > but no FeS cluster.
> > Does anyone have any idea what might be wrong? Since the MAD
> > alone phased map
> > looks fine I think there is nothing wrong with scaling or
> > having bijvoet pairs
> > flipped.
> >
> > By the way, I view the RESOLVE map in XTALVIEW by calculating
> > a PHS file from the
> > RESOLVE output with the following script, and viewing the
> > Fo*f.o.m. map (is this
> > wrong?):
> >
> > mtz2various HKLIN resolve.mtz HKLOUT resolve.phs << eof
> > OUTPUT USER  -
> > '(i3,2i4,4f8.2)'
> > labin  FP=FP FOM=FOMM PHIB=PHIM
> > end
> >
> > I have a seminar on Friday, and wanted to have the structure
> > properly phased by
> > then. Thanks!
> >
> > AGS
> >
> >
> > _______________________________________________
> > sharp-discuss mailing list
> > sharp-discuss@globalphasing.com
> > http://www.globalphasing.com/mailman/listinfo/sharp-discuss
> >

--
Paul Hubbard
Dept. of Biochemistry
Medical College of Wisconsin
Phone: 414-456 4305
Fax: 414-456 6510
URL: iris9.biochem.mcw.edu