Hi Peng Zhang,
The presence of radiation damage might cause some problems.
Do so see any obvious features in the difference map?
Another problem (although I doubt it would cause such a big difference) might be the fact that f' andf f" prime are incorrect.
Try and refine them (CNS or phenix.refine) maybe.
Does your native data have the same free set as the peak data? if not, you are in trouble and have to start from scratch with your native data to be able to make a fair comparison. The 22/25 for 2.7 A seems awfully close together.
procheck has not very up to date standards of what is good and what is not. Better use molprobity, available from:
http://molprobity.biochem.duke.edu/
HTH
Peter
----- Original Message -----
From: Peng Zhang <[log in to unmask]>
Date: Tuesday, March 20, 2007 6:04 pm
Subject: Re: [ccp4bb] modelling with sad/mad data
To: [log in to unmask]
> Maybe I did not make the questions clear, which leading to the
> misleadings.Firstly, I have collected the mad data and get the
> phase at synchrotron,
> the phased Se is quite good for modelling, and get over 70% of the
> molecule run with resolve autobuilding.The density seems also good for
> building. But when finally refining the model, the gap between the
> R(0.22)and free_R(0.32 )is big, even though modelled the Se-
> methionine. Before
> collecting the mad data at synchrotron, I already have another
> native data
> set collected at home diffractometer (rigku, with R-axis IV++). To my
> surprise, when I using the same model(first model) and run with
> this data
> set, it is quite good( with 2.7A resolution, R=0.24 and Rf=0.28 and
> further refine to R=0.22 and Free_R=0.25), and I got the final
> model.Thegeometry of the first model and final model(actually no
> big difference of
> the two models)is quite good with procheck.The omit map says good
> enoughwith both of the two models.
>
> So I wondering what happened with the peak data? Did the anomolous
> signalhave much effect on the data? and anyone have the similar
> experience?
>
> > First it is always best to refine your model against the highest
> > resolution good quality data that you have available. There was
> > correspondence about the geometric weighting - could you have
> weighted> the Xray data too high and have bad geometry - see
> previous Emails!
> >
> > And the Free R seems rather low for the Se data.
> > Did you transfer the same Free R set from the native to the Se data?
> > Eleanor
> >
> >
> > Peng Zhang wrote:
> >> Dear friends,
> >>
> >> Recently, I have solved a structure using mad method. When
> using the
> >> peak
> >> data(2.3A) as the native for structure refinement, the gap
> between R
> >> factor and R free is big, about 0.1(0.22 and 0.32). I modelled the
> >> selenomethionine but the gap still exists. When I changed the
> data for a
> >> real native one(2.7A),it seems OK with R=0.24 and Rf=0.28.
> >>
> >> Does anyone have the similar experience?
> >> what should I pay attention to when using the sad/mad data as
> the native
> >> one for modelling and refinement?
> >>
> >> Thanks in advance.
> >>
> >>
> >>
> >
> >
> >
>
>
> --
> Peng Zhang, Ph.D. Student
> Institute of Biochemistry and Cell Biology
> Shanghai Institutes for Biological Sciences
> Chinese Academy of Sciences
>
> 320 Yue-Yang Road
> Shanghai 20031
> P.R. China
>
>
>
> Tel: 021-5492-1117
> Fax: 021-5492-1116
> Email: [log in to unmask]
>
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