*** For details on how to be removed from this list visit the ***
*** CCP4 home page http://www.ccp4.ac.uk ***
Hi, Wu,
When you tried refmac, did you also try some different models for rigid
groups using TLS ? I have seen several cases where there were reasonable
displacements which could be modeled by TLS tensors, what led to a serious
decrease on the R factors.
( this will prompt me to raise one other question on the next e-mail
concerning docking ...).
Anyway, there are also other possibilites as other have pointed out.
Jorge
----- Original Message -----
From: "Wu Mousheng" <[EMAIL PROTECTED]>
To: "Juergen Bosch" <[EMAIL PROTECTED]>
Cc: <[email protected]>
Sent: Friday, August 25, 2006 11:38 PM
Subject: RE: [ccp4bb]: R and Rfree factor for 2.0 A model
*** For details on how to be removed from this list visit the ***
*** CCP4 home page http://www.ccp4.ac.uk ***
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
*** For details on how to be removed from this list visit the ***
*** CCP4 home page http://www.ccp4.ac.uk ***
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
DISCLAIMER:
This email is confidential and may be privileged. If you are not the
intended recipient, please delete it and notify us immediately. Please
do not copy or use it for any purpose, or disclose its contents to any
other person as it may be an offence under the Official Secrets Act.
Thank you.
--
Jürgen Bosch
Howard Hughes Medical Institute and
University of Washington
Dept. of Biochemistry, K-426
1705 NE Pacific Street
Seattle, WA 98195
Box 357742
Phone: +1-206-616-4510
FAX: +1-206-685-7002
DISCLAIMER:
This email is confidential and may be privileged. If you are not the
intended recipient, please delete it and notify us immediately. Please do
not copy or use it for any purpose, or disclose its contents to any other
person as it may be an offence under the Official Secrets Act. Thank you.
--
Esta mensagem foi verificada pelo sistema de antivírus e
acredita-se estar livre de perigo.
--
Esta mensagem foi verificada pelo sistema de antivírus e
acredita-se estar livre de perigo.
