[phenixbb] question on molecular replacement

fn1 at rice.edu fn1 at rice.edu
Mon Jun 11 07:49:28 PDT 2012

Thank you very much! The ab initio method may be worth trying first.

Quoting Andrew Purkiss-Trew <Andrew.Purkiss-Trew at cancer.org.uk>:

> For this resolution and type of problem, generating a  
> Selenomethionine derivative is probably overkill.
> Firstly, you can try abinitio methods such as Archimboldo  
> (http://chango.ibmb.csic.es/ARCIMBOLDO/), which can work on  
> 2Angstrom data given a helical structure.
> Secondly, try generating derivative datasets. So, for example,  
> Potassium Iodide may bind to the helices and give good anomalous  
> phase information even on a home source. SIRAS can then be used to  
> solve the structure. You will need to spend some time getting a good  
> derivative, but it is generally quicker and cheaper than producing  
> SeMet protein.
> Good Luck,
> Andrew Purkiss.
> X-ray Lab Manager
> London Research Institute.
> ________________________________________
> From: phenixbb-bounces at phenix-online.org  
> [phenixbb-bounces at phenix-online.org] On Behalf Of Machius, Mischa  
> Christian [mischa_machius at med.unc.edu]
> Sent: 11 June 2012 14:19
> To: PHENIX user mailing list
> Subject: Re: [phenixbb] question on molecular replacement
> Besides what others said about the technical aspects of your  
> molecular replacement endeavors:
> Gel filtration is not the most accurate method to determine  
> oligomeric status. Also, the content of the asymmetric unit may or  
> may not have anything to do with the oligomeric status of a protein.  
> So, best not to pay too much attention to that. First, try to find  
> four copies, then another one, if there is still space and there is  
> electron density indicating another molecule.
> More importantly, designed structures often deviate significantly  
> enough from 'real structures that molecular replacement becomes  
> difficult or impossible. There is great satisfaction to be derived  
> from a designed molecule being suitable as a search model in  
> molecular replacement, but in the end you'd really want an  
> independently determined structure. I assume that part of the  
> motivation behind determining the crystal structure of your protein  
> is to verify your design. If so, a completely independent structure  
> would be desirable and would also convince any reviewer. Thus, I  
> would recommend generating the seleno-methionine variant of your  
> design (provided it contains any methionines) and solving it  
> experimentally.
> Best of luck!
> MM
> On Jun 10, 2012, at 10:57 PM, <fn1 at rice.edu>
>  wrote:
>> Hi everyone,
>> I have a dataset in P21221. The cell content analysis shows that  
>> there should be 5 monomers in asu. The gel filtration profile of  
>> this protein shows that it should form a tetramer.
>> I have a simulated structure as searching model. I try to use the  
>> whole model or backbone model, and different resolution cutoff.  
>> When the whole model is used, the llg of solution is negative. When  
>> the backbone model is used, the llg is about 160 when searching for  
>> 4 monomers and tfz is 7.4. But the following autobuild process  
>> could not lower rfactor than 50%.
>> I notice online that it might be useful to run self rotation  
>> function first to find ncs operators before doing mr. Is this true  
>> and how can i do this?
>> Thank you in advance!
>> Fengyun
>> _______________________________________________
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>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
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