Dear Rajnesh,
I wonder about your chosen space group?
I commend that you expand your diffraction data into P1, then run molecular 
replacement with Phaser in P1 and if a solution is determined by Phaser run the 
coordinates through Zanuda to determine the space group.
Best wishes,
John 
Emeritus Professor John R Helliwell DSc




> On 12 Feb 2020, at 07:23, Rajnesh Kumari Yadav <rajn...@rcb.res.in> wrote:
> 
> Hello everyone,
> 
> I am working on a protein which have 5 domain in it, we have its 4 domain 
> structure and 3.0 Angstrom data of 5 domain protein crystal. While doing the 
> Molecular replacement we got solution with four domain with good electron 
> density and space for last domain without any density. When we tried 
> Molecular replacement with the missing domain (modelled) only we got solution 
> shows density for this missing domain but not able see electron density for 
> rest four domain even though room for 4 domain was visible in the solution. I 
> need help or suggestion for this issue.
> 
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