Hi,
If you have density for the protein and the DNA and the density for
the protein is correct and you see left-handed DNA density, then I
suppose you are seeing Z-DNA?
Doesn't seem like a problem of incorrect enantiomorph if your protein
density is fine. You can pull out a Z-DNA structure from the PDB and see
if you can get a fit into the density that you see and if it makes sense
you can then try to build an idealized Z-DNA based on the sequence you
used for crystallization.
Regards,
Debanu.
Green, Todd wrote:
Hello Ruchi,
I know that when you use non-crystallographic averaging there is a
possibility of the starting with positive density and ending up with
negative, the enantiomorph, or the negative enantiomorph density. In
order to shift back to the correct phases you can apply a simple
formula. This is the math that i recall:
positive structure alpha
negative structure alpha + 180
enantiomorphic structure -alpha
negative enantiomorphic structure -alpha + 180
The recollection comes from a paper in methods in enzymology that i
don't recall the author or year of at the moment.
I know your case has nothing to do with averaging but the math should
hold true. In this case, you can switch between the enantiomorphs by
multiplying the phases by -1. I don't know if this holds a solution to
your case. It may be worth a quick shot just to multiply the phase
column by -1. I may be far off base here but i think i am correct.
This of course is assuming that you have the correct space group and
that you have the enantiomorphic phases.
If i am totally off on this, someone please correct me. I'm really
sticking my neck out late on a friday, eh!
Good Luck-
todd
-----Original Message-----
From: CCP4 bulletin board on behalf of Ruchi Anand
Sent: Fri 3/30/2007 5:31 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Right Handedness of Density
Dear All,
We are working with a DNA binding protein with 4 Zn sites in in ASU.
Using SnB and then CNS we were able to get a map using MAD phasing and
could visualize the density for the double helix of the DNA but it was
a left handed spiral instead of the usual right handed one. The space
group which yielded the result was P3(2). We tried to flip the sites
and change the space group to P3(1) but we are not able to generate a
sensible map. Any advice regarding the best way to proceed will be
very helpful. The resolution is around 3.2.
Thanks
Ruchi
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