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Re: [cnsbb] Molecular replacement

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  • Chris Bystroff
    I once had a similar problem. In your case, the protein is fused so you know it is there. I suggest you get initial phases from the MBP molecular replacement
    Message 1 of 2 , Feb 10, 2013
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      I once had a similar problem. In your case, the protein is fused so you know it is there. 

      I suggest you get initial phases from the MBP molecular replacement solution. Then use iterative skeletonization to find the remaining density. Skeletonization works with 3A data.  

      Here's reference to the algorithm Skeletonization is included in the CCP4 package. I am not sure about whether it is in  Phenix.

      Baker D, Bystroff C, Fletterick RJ & Agard DA. (1993). PRISM: topologically constrained phase refinement for macromolecular crystallography.

      Bystroff C, Baker D, Fletterick RJ & Agard DA. (1993). PRISM: application to the solution of two protein structures. Acta Crystallographica, Section D (Biological Crystallography) D49, pt.5, 440-8.

      --Chris

      On Feb 10, 2013, at 2:52 PM, Tewary Sunil wrote:

       

      HI

      I have MBP fused protein. I got the x-ray data at 3.1 A resolution. I have solved the MBP structure with the MBP as a model. I can see the density (Fo-Fc)for the fused protein in the unit cell very clearly. I have a one molecule in the unit cell (P31 2 1). The model for my protein is very poor has only 16% identity. When i put the MBP and my protein model in the phaser, the phaser immediately gives the solution for the MBP rejecting the other model. If i give my model only it keeps on searching forever.

      Has anybody face such type of problem? If so, how to solve the structure?

      Any suggestions would be appreciated.


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