Re: [ccp4bb] Molecular replacement of a multidomain protein

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CCP4bb <-- 2008 <-- March 2008 <-- 07 March 2008

Previous message:
Subject: Re: Molecular replacement of a multidomain protein
From: Lucas Bleicher lbleicher {- at -} YAHOO {- dot -} COM
Date: 2008-03-07

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Subject: Re: Molecular replacement of a multidomain protein
From: "Meyer, Peter" pameyer {- at -} MCW {- dot -} EDU
Date: 2008-03-07

Subject: Re: Molecular replacement of a multidomain protein
From: Roger Rowlett rrowlett {- at -} MAIL {- dot -} COLGATE {- dot -} EDU
Date: 2008-03-07

EPMR (now Open-EPMR, http://www.epmr.info) is an excellent alternative
for finding difficult, high-dimensional MR solutions. Experiment with
various resolution limits. We solved an asymmetric unit with 3
difficult-to-place dimers of low sequence homology by gradually
increasing the high-resolution limit of the structure factor data used.
If you have a partial static solution, it can look for additional
protein chain placements. It is strongly recommended for your type of
problem that you set the correlation coefficient threshold for a good
solution to 1.00 and not use the defaults. This will force EPMR to do an
exhaustive search.

Cheers,

--
------------------------------------------------------------------------
Roger S. Rowlett
Professor
Colgate University Presidential Scholar
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346

tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: rrowlett@mail.colgate.edu

Lucas Bleicher wrote:
> I've had a very good experience with MrBump:
>
> http://www.ccp4.ac.uk/MrBUMP/
>
> Not only because of the program itself, which was able
> to find an unexpected template for the problematic
> chain (the first one was straightforward in Phaser),
> but also because of great support from Martyn & Ron.
> It's definitely worth a try.
>
> Lucas
>
> --- Anjali Mehta escreveu:
>
>
>> Dear All,
>> I am working with a Bifunctional protein of
>> molecular weight ~60 kDa.
>> I have a 3.3 angstrom native dataset. The matthews
>> number show there are 6
>> molecules in the asymmetric unit.
>> The structures of the individual domains are already
>> known from prokaryotes.
>> The sequence identity with the known structures are
>> about 30%.
>> I have tried molecular replacement using the two
>> parts as models
>> respectively with CNS, MOLREP, PHASER etc. However I
>> always get the solution
>> for one domain. I have also tried to fix that domain
>> and find the other one.
>> But none of the programs can find a solution.
>> I am trying to model build the correct sequence of
>> one domain using a
>> density modified (using CNS), NCS averaged (using
>> RAVE) map but the map does
>> not look very good. The side chains are not clear.
>> That might be due to the
>> fact that I am only having a partial model.
>> Any suggestion will be appreciated.
>> Thanks.
>> Ms. Anjali Mehta
>>
>>
>
>
>
> Abra sua conta no Yahoo! Mail, o único sem limite de espaço para armazenamento!
> http://br.mail.yahoo.com/
>

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CCP4bb <-- 2008 <-- March 2008 <-- 07 March 2008

Previous message:
Subject: Re: Molecular replacement of a multidomain protein
From: Lucas Bleicher lbleicher {- at -} YAHOO {- dot -} COM
Date: 2008-03-07

Next message:
Subject: Re: Molecular replacement of a multidomain protein
From: "Meyer, Peter" pameyer {- at -} MCW {- dot -} EDU
Date: 2008-03-07