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CCP4BB  February 2007

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Subject:

Molecular replacement and refinement trouble

From:

Jenny <[log in to unmask]>

Reply-To:

Jenny <[log in to unmask]>

Date:

Fri, 2 Feb 2007 21:37:37 -0500

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (33 lines)

Hi, Dear all,

Firstly ,I'd like to thank all the people for their kind help,
especially Miguel, Bernie ,Mark, Moody, Eleanor, Eaton , Peter and
lots of others ....Without your help, I wouldn't make it this far.

Secondly, I'd like to share some of the experiences. We had a hard
time trying to do MR for this protein. The data was indexed very well
in R32, and we can only find two molecules,we just couldn't find the
other.We stocked for a long time, not until recently, we figured it's
actually  a C2 space group. But when we tried to search with one
monomer, we couldn't find the solution either because the signal is
really low.So we search by those two molecules ( from R32 ), and
bingo, we found 6 molecules.So on and so forth, now we are able to
find 9 molecules and we believe that's all.Three molecules are bundled
together and form three trimers and these three trimers are 3-fold
symmetry related.We were excited and went for the next step
refining...But after rigid body refinement, the Rfree is still very
high , 44%.We calculated the map and looks like density around one
loop region is incomplete.I was told that I should give this up,
because there is no way to build the model because the density is
missing. But I was just wondering if there are any better ways to do
refinement, is there any way that could possibly determine the
structure.The data is 2.1A,but my protein is really small, 10kD, looks
like the packing is really not that great.We are now using CNS to do
the refinement.

Any suggestions would be highly appreciated.

Thanks.

Jenny

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