[ccp4bb] Maps look different from auto-mtz vs EDS vs FFT in Coot or CCP4MG.

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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From: Roger Rowlett RRowlett {- at -} MAIL {- dot -} COLGATE {- dot -} EDU
Date: 2007-05-24

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Subject: Maps look different from auto-mtz vs EDS vs FFT in Coot or CCP4MG.
From: Kendall Nettles knettles {- at -} SCRIPPS {- dot -} EDU
Date: 2007-05-24

I¹d like help in interpreting some mystery density in a structure.

I¹m writing a paper about soaking the apo-estrogen receptor with different
ligands. The apo structure is already released, as pdb code 2B23. The
question is whether there is a mystery molecule in the pocket of the apo
receptor. If you superimpose 3ERD, you can see where the ligand binds. The
problem is that with some maps the pocket appears completely empty, and with
others, there appears to be something there. Protein looks essentially
identical with the different maps. We have used a few different approaches
to identify the compound with LC-MS, and are pretty sure there is nothing
there. For example, we can bind our protein to beads, soak it with
estradiol, wash extensively, elute with organic solvent and find a great
peak for estradiol, but nothing for the apo protein. We have also tried
non-denaturing MS.

If you look at the 2mFo-DFc map from EDS in Coot or CCP4mg, you see mystery
density in the pocket. If I use the MTZ, you see density in Coot, but not
CCP4MG. I then downloaded the structure factors from the PDB and made an
MTZ. The map in CCP4MG shows some density, but much less that with the map
from EDS. When I used FFT to make a 2mF1-1nF2 map, there is no mystery
density in either CCP4MG or coot.

I was ready to submit the manuscript with a picture of the mystery density,
but now I¹m not sure if that is appropriate. Any suggestions, as far as how
to interpret this mystery density would be greatly appreciated.

Best Regards,
Kendall
--
Kendall W. Nettles, PhD
Assistant Professor
Department of Cancer Biology
The Scripps Research Institute
5353 Parkside Dr.
Jupiter Fl 33458

office 561-799-8851
fax 561-799-8805
cell 561-306-7566

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: another quick question...
From: Roger Rowlett RRowlett {- at -} MAIL {- dot -} COLGATE {- dot -} EDU
Date: 2007-05-24

Next message:
Subject: removal of sulfate ion from the active site
From: Yue Li yl392 {- at -} CORNELL {- dot -} EDU
Date: 2007-05-24