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Dear all,
Thank you very much for your replies.
The spacegroup of my crystal is p212121. The data was processed with D*TREK. I
soaked my crystal in KI and collected the data using in-house x-ray machine. I
used SnB to find the position of heavy atom (I) and refined the heavy atom and
did solvent flatten in SHARP. The model was auto-built using ARP/WARP in CCP4.
Then I manually revised the model in Program O.
I have checked the logfile of TRUNCATE. It seems no twining in my crystal. I
also have tried to refine my model in Refmac5 with restraint refinement and it
seems no improvement in R factors.
Any further suggestions?
Thanks in advance!
Best
Mousheng Wu
-----Original Message-----
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Juergen Bosch
Sent: Saturday, August 26, 2006 12:12 AM
To: Wu Mousheng
Cc: [email protected]
Subject: Re: [ccp4bb]: R and Rfree factor for 2.0 A model
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Hi Mousheng,
what's your space group ? Are you certain you are in the correct space
group ? How did you solve your structure ? De novo or MR,. if MR have
you tried composite omit maps and ensured that what you have modeled is
indeed correct and not model bias from the MR solution ? Is there a
significant drop in I/sigI ? Then you might use that as your resolution
cutoff - data processed with HKL, Mosflm or XDS ?
Juergen
Wu Mousheng wrote:
> Dear all,
>
>
>
> I am refining my model with 2.0A using CNS. I have fitted most of the
> protein sequence into the model (150 of 160 aa). I also added 100
> water molecules into the model. The final R and Rfree factor are about
> 26% and 28%, respectively. I am wondering why I can not refine my
> model to low R and Rfree factors below 25%. The geometry of my final
> model is very good. 96% residues are in most favorable region.
>
>
>
> I think my data is quite good. I/sigma(unaverage) and completeness at
> highest resolution shell is 2.3 and 99%. Rmerge is about 6%.
> Redundancy is about 5.
>
>
>
> Is my model acceptable based on the R and Rfree factors? Is there any
> reason for the high R and Rfree factors?
>
>
>
> Thanks!
>
>
>
> Best,
>
> Mousheng Wu,
>
> Institute of Molecular and Cell Biology, Singapore
>
>
>
>
>
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>
--
Jürgen Bosch
Howard Hughes Medical Institute and
University of Washington
Dept. of Biochemistry, K-426
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Seattle, WA 98195
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