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Re: [ccp4bb] Question about strange MR solution
 

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CCP4bb <-- 2008 <-- February 2008 <-- 05 February 2008
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Subject: Re: Question about strange MR solution
From: Pietro Roversi pietro {- dot -} roversi {- at -} PATH {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2008-02-05 		Next message:
Subject: Re: an over refined structure
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2008-02-05


Subject: Re: Question about strange MR solution
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2008-02-05
I think you have just found a symmetry equivalent of your original
structure solution.

In P6122 there are 12 possible symmetry operators to choose from - only
one of which will be the identity (equivalent to alpha=beta=gamma=0)
One certainly will have alpha or gamma = 180, and beta 0, equivalent to
-x,-y,z
Then you could also have found a solution on the alternate origin (0,0,0.5)

I use lsqkab ( superpose molecule task) to fit the solution to the
original and look at the matrix to convert 1 to the other
It should match one of the symmetry operators of P6122

Eleanor




Michele Lunelli wrote:
> Dear all,
>
> I refined a protein structure in the space group P6(1)22, with one
> copy in the asymmetric unit, resolution ~1.8 A, Rwork=0.20, Rfree=0.22.
> Then I tried to feed Phaser (version 1.3.3) with this structure. It
> found quickly a very prominent solution, but the first euler angle is
> 180 instead of 0 degrees (the others are 0, as well as the fractional
> coordinates). This solution is not symmetry-related with the structure
> that I used as search model: indeed, there are a lot of clashes.
> However, when I refine this solution, I obtain immediately R factors
> as good as the search model, and also the electron density map looks
> perfect. Of course, I used the same reflections file to refine the
> initial structure and the MR solution rotated of 180 degrees.
>
> How can I explain this? The analysis with Truncate (moments and
> cumulative intensity distribution) don't suggest any twinning, as well
> as the Padilla-Yeates test. Is it possible, that I refined the
> structure in the wrong space group?
>
>
> Thank you in advance,
>
> Michele Lunelli
>
>

CCP4bb navigation

CCP4bb <-- 2008 <-- February 2008 <-- 05 February 2008
Previous message:
Subject: Re: Question about strange MR solution
From: Pietro Roversi pietro {- dot -} roversi {- at -} PATH {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2008-02-05 		Next message:
Subject: Re: an over refined structure
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2008-02-05


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