Dear All,
Thank you Folmer and Fred for your suggestions. Mine is
an isomorphous crystal. I had refined without using the
same set of Rfree reflections, finally getting larger
difference between the R and Rfree. I hope considering
the same Rfree set would solve this problem.
Thank you
With regards
Kavya
> Although it is not "mandatory", I think it would be a very good idea,
> especially if you have the exact same spacegroup and the native and
> ligand-bound forms of your protein are essentially the same.
>
> If you do not use the same reflections, you are actually not reporting an
> independent (free) R-factor.
>
>
>
>
> Best regards,
> Folmer
>
>
>Hello,
>
>I think this depends on the type of problem you are facing:
>
>if the 2 crystals are not isomorphous then you cannot have the same
>R-free sets;
>if the 2 crystals are isomorphous then either you do not worry about
>keeping the same R-free set (but then the starting structure must be
>"perturbed enough" to get rid of R-free bias during refinement), or you
>keep the same indices for the reflections in the 2 R-free sets ("same
>reflections" in your message) in which case there is no R-free bias at
>the beginning of refinement.
>
>By R-free bias I mean this: in your "new" (liganded) crystal form, there
>are reflections that "have seen the Fo's" during refinement of the
>native structure but that are in the R-free set in the ligand structure.
>This leads to bias.
>HTH,
>Fred.
>> > Dear users,
>> >
>> > Is it mandatory to use the same reflections for
>> > Rfree calculations of a ligand bound data as that
>> > of its native?
>> >
>> > Thank you
>> > With Regards
>> > Kavya
>> >
>> >
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