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

- Protein crystallography

Main steps:

- Protein purification
- Crystallisation

Special:

- Programs for crystallography
- X-ray detectors

Basic tutorials:

   - Chemistry
   - Protein
   - Peptide
   - Amino Acids

Xtal community:

- CCP4BB

CCP4bb navigation

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

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

Next message:
Subject: AW: removal of sulfate ion from the active site
From: Herman {- dot -} Schreuder {- at -} SANOFI-AVENTIS {- dot -} COM Herman {- dot -} Schreuder {- at -} SANOFI-AVENTIS {- dot -} COM
Date: 2007-05-25

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

Dear Kendall,
I would suggest you to run a simulated annealing omit map around the
region you are interested.
The model bias will be reduced and you will get a more clear answer.

Ciao,
Joao

Joao M. Dias
Ollmann Saphire Lab
The Scripps Research Institute
10550 North Torrey Pines Rd. IMM-2
La Jolla, CA 92037 USA
tel (858)784-8925

On May 24, 2007, at 9:57 AM, Kendall Nettles wrote:

> I’d like help in interpreting some mystery density in a structure.
>
> I’m 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 I’m 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: removal of sulfate ion from the active site
From: Yue Li yl392 {- at -} CORNELL {- dot -} EDU
Date: 2007-05-24