Although there might be space group and twining trouble from the sound
of it, running ARP/wARP starting from your molrep solution, at that
resolution should really do whatever can be done and reduce R/RFree
while building the vast majority of the model. If Rfree stays high,
start looking at sg possibilities and twining.
A.
PS In general I would suggest to download and install arp/warp but a
quick try for new users can always be through the web interface
http://cluster.embl-hamburg.de/ARPwARP/remote-http.html
On Feb 7, 2011, at 11:49, Md. Munan Shaik wrote:
Dear all,
I have a question regarding the refinement and density map.
My protein is 261 amino acids long and crystalize very nicely with
very high resolution . There is no multiple spot in the image and
diffraction looks amazing. I collected a dataset at 1.38 resolution
and the space group is P43, overall Rmerg is 0.02 (most likely the
space group is P4122, but then the solvent content is less than 16%
for one molecule in the assymmetric unit, that are unlikely), so I
processed the image in P4 (36% solvent) and run molecular
replacement with a model that have 42 sequence identity. I got a
solution in P43 that are good enough in some part but in the map
there are many gap at even lower sigma level. I tried to refine and
Rfree stacked at 36 along with Rwork, which is 33.
I also checked the degradation patteren of the protein in the
crystal and it looks not degraded and full length protein crystalize.
Is there anybody can suggest me anything that I can try?
Regards,
Md. Munan Shaik
PhD Student
Department of Biotehnology
School of Bioscience and Biotechnology
via G. Colombo 03
Padova 35131, Italy
Mobile: 00393275671896
E-mail: munanbt2...@yahoo.com
munan.sh...@unipd.it
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Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member
Department of Biochemistry (B8)
Netherlands Cancer Institute,
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