Re: [ccp4bb]: strange NCS/refinement problem (twinning?)

[Dima Klenchin <klenchin@facstaff.wisc.edu>]

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At 05:00 PM 9/13/2002 -0700, Sarah G. Hymowitz wrote:
>Dima,
>	If you leave out the bad copy entirely, do you get similar statistics and 
>does any meaningful difference density appear?  

If I leave out bad copy, I think refinement still goes reasonably 
well - map looks acceptable and there is density for ligands on
difference map. R factors are ~ 5% higher but I guess it is to be 
expected. 

>It may be that your 
>current solution is correct but that the badly ordered copy s just 
>that-- badly ordered.  What's the packing like?  Does the poorly ordred 
>copy make fewer crystal contacts? 

It is not obvious to me that it does. Packing is indeed pecular -
sort of zigzagging sheets composed purely of molecule A (good one)
alternating with parallel but more even sheets composed of 
molecule B (bad one). 

>I have heard of cases like this where 
>one domain or copy is just much more poorly ordered that the rest of the 
>unit cell.  

I heard it can happen. Being a crystallography novice I am 
just not sure how to deal with it properly and how to eliminate
all other possibilities (if any!). Sounds too esoteric to me 
to just let it go without thorough investigation. 

>Since you are lucky and have good maps etc for one copy and 
>your refinements statistics are proceeding well, can you base your 
>analysis on the well ordered copy?

:-) In fact, 99.9% of relevant biological information is probably 
already there. Yet I am not sure what I am supposed to do as far 
as crystallographic standards are concerned. 

>good luck,

Thanks! 

Dima


>Sarah Gillmor Hymowitz
>
>Dima Klenchin wrote:
>> ***  For details on how to be removed from this list visit the  ***
>> ***          CCP4 home page http://www.ccp4.ac.uk         ***
>> 
>> Hello all, 
>> 
>> I am facing a problem I am not sure how to address. 
>> how to approach (short of looking for a different xtal form). 
>> 
>> Good data set to 2A, indexes very well by P2 (67.947 76.813 98.441, 
>> beta=101.21) or P1 (alpha and gamma within 0.5 close to 90). 
>> Two molecules per cell. Scaled as P2, systematic absences indicate
>> P21 very clearly. 
>> 
>> Molrep finds what appears to be a good solution readily. Problems
>> start after that: When I restrain or constrain NCS during refinement, 
>> R free goes way up (R~30, Rfree > 40%). If I refine without NCS, 
>> R factors slip right away to 27/29 but this strange thing 
>> happens: one copy of the protein refines very well - low B factors,
>> very good looking map, two ligands totalling >100 non-H atoms
>> show up perfectly well on 1fofc map. A completely different 
>> story with another copy of the molecule: B factors are sky 
>> high and the map looks crappy with most of it being probably
>> model bias. Matthews coefficient is 6.1 with just one molecule...
>> 
>> At this point I have tried a lot of things hoping to find 
>> an error in previous steps and nothing shows up. Can this be
>> twinned crystal? Yates server does not appear to think so. 
>> Short of trying to find a new well-diffracting crystal form,
>> is there a reasonale solution? 
>> 
>> Thanks so much for any help, 
>> 
>> Dima
>> 
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