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Hi Mousheng,
Hmmm... Have you looked at the Rfac and Rfree vs resolution table in the
logfile to see if there a sharp increase in Rfac/Rfree at any
resolution? Even if all iodines are accounted for, how about metals/ions
etc. in your crystallization solution?
Can you build any more waters? Are you using CNS to pick your waters?
Often, I have to go through multiple rounds of water picking and throw
many that CNS finds even in the first round. Alternative side chain
conformations?
Just some thoughts.
Raji
Wu Mousheng wrote:
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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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