Re: [ccp4bb]: molecular replacement woes!

["Eleanor J. Dodson" <ccp4@ysbl.york.ac.uk>]

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schakrav wrote:
> 
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> 
> hi,
> my name is srinivas chakravarthy (cheenu) and i am a graduate student in
> Dr.Karolin Luger's lab at Colorado State University. I am an absolute beginner
> in the field of crystallography and would deeply appreciate any input that
> comes my way pertaining to the problem i am now facing which is-
>    I have synchrotron data from a nucleosome crystal which was indexed and
> scaled without any major problems in the space group p222(1). I get an overall
> completion of 96.7%. I run into problems at the molecular replacement stage
> (using CNS). the spacegroup of the model is p2(1)2(1)2(1). when i do a cross
> rotational search, going by the rotation function peak height values it seems
> to have worked. (highest values are .1591 and .1496 and the rest of the values
> are in the .06 range). this is on using "fastdirect". i havent tried "direct".
> when i do a translational search i do get a solution with a correlation
> coefficient (E2E2) which is significantly higher than the other solutions
> (monitor no. is .262) but on minimization refinement i get unreasonable r and
> free_r values. my final r is 0.5163 and the final free_r is 0.5231. the model
> and my molecule supposedly have a high degree of homology.
> my questions are 1.should i expect problems in molecular relacement on account
> of the model and my molecule being in different space groups (i've been told
> that i shouldnt)? if so what would be the nature of the problem? 2. what could
> be the possible reasons for the high r and free_r values?
> Do forgive the lack of precision in expressing my problem. My excuse is I am
> just beginning to use the terminology and the concepts.
> thanks for your patience,
> cheenu.
> 
> Srinivas Chakravarthy
> Colorado State University
> Fort Collins
> CO-80521

 Consider whether you could have a different space group.
How clear is it that the space group is P212121 and not P21212 or some
other variant?

 You should ALWAYS process data without assuming screw axes ie process
any P2i 2i 2i crystal as P222 and look at the values of reflections
along 00l 0k0 and h00 to decide whether they are screw axes. Sometimes
the information is misleading - one set may be missing or incomplete. 


 Then if there is ambiguity do the MR search in all the possibilities.
You should get the best score in the correct space group of course, but
reasonable scores in alternate ones, because half the reflections ( eg
all the 00 2l  set are not affected if the space group were P 21 21 21
or P 21 21 2.)

 Eleanor