[phenixbb] unusual maps and Rfree for 1.75 structure

Pavel Afonine pafonine at lbl.gov
Sat Apr 16 22:15:08 PDT 2011

Hi Yuri,

you did not mention the resolution... From your email I guess it is 
1.9A, is it correct?

Anyway, to bypass the uncertainties of the space group choice (and 
artifacts due to constraints it applies) you can always process your 
data in P1, solve and refine you model (applying NCS if necessary; and 
yes, you are not solving completely new structure - you solved it many 
times before, so you know the answer pretty much!) and see how the 
solution obtained this way compares with whatever else you get from more 
wise strategy.


On 4/16/11 7:50 PM, Yuri wrote:
> I am solving a structure of an enzyme that I have solved many times 
> before, the only difference is a single mutation in the active site.
> The crystal grew in basically exact conditions (macroscopically 
> speaking they look different) as the other mutants I had. I scaled the 
> data P 43 21 2 Rsym 0.068.  Like all the other data sets I had before.
> This time however, the initial model has Rfree of about 0.27 and the 
> maps look more like those of a 2.5 - 2.8 structure. My experinence 
> with this enzyme is that I should be looking at around 0.22 or lower 
> Rfree, and pretty clear maps as I saw for my 1.9 structure. Xtriage 
> does not detect any pathologies.
> I rececked my scaling log file, and it lists the systematic absences 
> for the data.
> I see some that are not that "weak"
> for instance :
> h k l      I/sigma
> 0 0 1        6.0
> 0 0 2        5.8
> 0 0 13       7.8
> So I am inclined to reprocess my data in P 4 2 2. Are these "symptoms" 
> of a possible wrong space group assignment? Is there something else 
> obvious I am overlooking?
> Thank you
> -- 
> Yuri Pompeu
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb

More information about the phenixbb mailing list