[phenixbb] phaser MR

[Francis E Reyes]

Shya,

Did phaser complain that the asymmetric unit was too full?  How do the  
self rotation maps look? Are the crystallographic peaks exact or off  
by a few degrees (your resolution data may make it difficult to see  
this)? How do the N(z) cumulative intensity distributions look (make  
sure to calculate this with thin resolution bins, i.e. increase BINS  
in Scala I think)? Does your data look sigmoidal on this plot?

Perfect twinning or an NCS that's close to a crystallographic axis is  
difficult to diagnose from merged intensity statistics and even more  
difficult with resolution worse than 2.5. I recommend Dauter Acta  
Cryst (2003) D59 2004-2016 for a good discussion of this.

Your space group might be too high. See the subgroups of P422 at http://cci.lbl.gov/~phzwart/p422_2.png 
. Reintegrate and merge the data in each space group, MR a single copy  
of your model  (let phaser complete the ASU) and compare the Rpim's  
(from scaling/merging) and the Rwork/Rfree from a rigid body refine  
without NCS, with NCS, with appropriate twin laws, and with twin laws  
+ NCS. No need to do a full refinement just yet.  Allow phenix.refine  
to create the Rfree flags. Choose the space group which gives the best  
statistics.

I recently had a case (Hardin, Reyes, Batey J. Biol. Chem., Vol. 284,  
Issue 22, 15317-15324, May 29, 2009) of a protein that merged into  
P422 but was difficult to refine in that space group. I brought it  
back to P4 and refined with NCS+twin to give more reasonable Rwork/ 
Rfree (5-7% difference from the P422 to P4).

HTH,

FR



On Jul 23, 2009, at 3:54 PM, sbiswas2 at ncsu.edu wrote:

> Hi Francis,
> Thanks for your response. The matthews coefficient suggests two  
> molecules
> in the AU. Phaser also finds two molecules. I ran the dataset through
> phenix xtriage it did not indicate twinning though. The molecule also
> exists in nature as a monomer.
> Shya
>
>
>> Twinning? What's your matthews coefficient say? Do you know if your
>> structure is a multimer (biochemistry, etc)? Does  it agree with the
>> matthews coefficient?
>>
>> If the unit cell is  not big enough to hold all of the contents,then
>> this is an indicator for twinning .
>>
>> FR
>>
>> On Jul 23, 2009, at 3:09 PM, sbiswas2 at ncsu.edu wrote:
>>
>>> Hi all,
>>>
>>> I was trying to solve a structure by molecular replacement. I scaled
>>> the
>>> data in P4222 space group (resolution 2.7A) with two molecules in  
>>> the
>>> assymmetric unit (molecule A and B) I ran phaser with my model and
>>> got a
>>> Zscore of 5.1. When I look at the map that I got from phaser I could
>>> easily see good electron density for both molecules, However upon
>>> inspection of the electron density map there were considerable
>>> interaction
>>> or clashes with molecule B and a symmetry atom. Molecule A had no
>>> clashes
>>> however with the symmetry atoms. I was wondering if anyone knows how
>>> to
>>> resolve this.  Could it be a problem of space group. The statistics
>>> are
>>> good for space group P4222 and the I/sigI was good till 2.7A.
>>> Any advice is appreciated,
>>> Shya
>>>
>>> _______________________________________________
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>
>> ---------------------------------------------
>> Francis Reyes M.Sc.
>> 215 UCB
>> University of Colorado at Boulder
>>
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---------------------------------------------
Francis Reyes M.Sc.
215 UCB
University of Colorado at Boulder

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