[phenixbb] Autosol: MIRAS

ash.k at aol.com ash.k at aol.com
Wed Sep 5 20:07:04 PDT 2012


Yup, I have tried anisotropy truncation...
 

 

 

-----Original Message-----
From: Shya Biswas <shyabiswas at gmail.com>
To: PHENIX user mailing list <phenixbb at phenix-online.org>
Sent: Thu, Sep 6, 2012 8:32 am
Subject: Re: [phenixbb] Autosol: MIRAS


Hi AK,
Generally Se incorporation is not good at the N-terminus but since you
have six you should be able to locate the other three even at 4.8A.
Did you try using the anisotropy server, this might help you improve
the map, here's the reference:
http://www.pnas.org/content/103/21/8060.full
Shya

On Wed, Sep 5, 2012 at 10:08 PM,  <ash.k at aol.com> wrote:
>
>
> Hi Shya,
>
>  I did wavelength scan, got a good signal for Se and used appropriate
> wavelengths for data collection and also used experimental f' and f'' values
> for phasing. I think the reasons SAD or MAD for SeMet data is not working
> are (i) low resolution: 3.7 for SeMet (Anomalous data is up to 4.8A) (ii) I
> should have mentioned this earlier: 3 out of 6 Se are very close to
> N-terminus, possible they are disordered. Unit cell is also some what
> big..100, 120 and 320A; F222 space group.
>
> AK
>
> -----Original Message-----
> From: Shya Biswas <shyabiswas at gmail.com>
> To: PHENIX user mailing list <phenixbb at phenix-online.org>
> Sent: Thu, Sep 6, 2012 7:29 am
> Subject: Re: [phenixbb] Autosol: MIRAS
>
> Hi AK,
> Did you do a wavelength scan when you collected the SE dataset you
> need to put the values of f' and f'' from your wavelength scan in
> order to locate the heavy atom sites, 6 methionine should be enough to
> phase your molecule.
> Shya
>
> On Wed, Sep 5, 2012 at 9:25 PM,  <ash.k at aol.com> wrote:
>> Hi all,
>>
>> I am trying to solve a structure through experimental phasing using
>> AUTOSOL.
>> I have a couple of heavy atom derivative datasets (Hg, La, Eu, Cd) and
>> also
>> a SeMet data. Unfortunately all the datasets are of low resolution
>> (3.7-4.2A) and there are possibly 4-8 molecules in the asu. MIR, SAD and
>> MAD
>> alone did not give any convincing solution.
>>
>> However, MIRAS, with a combination of few heavy atom datasets and the
>> anomalous data from SeMet crystals, gave a somewhat satisfactory map. But
>> the heavy atom site picked by AUTOSOL list only one of the heavy atoms
>> i.e.
>> Lanthanum. In another set of run, the solution of which was not
>> convincing,
>> the heavy atom substructure had only Hg. There are 6 Met out of 200
>> residues
>> in one molecule and mass spec results show that Se incorporation is 100%.
>>
>> Now, my doubt is that why does the heavy atom substructure contain only La
>> and how can I get the substructure involving Se from this solution (or the
>> datasets used)?  Se location is going to help me a lot for finding a
>> starting point to assign side chains.
>>
>> Any suggestion would be greatly appreciated.
>>
>> Thanks
>> AK
>>
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