Hi,
Did you do rigid body refinement or regular minimization? If over
half your structure is missing, anything besides rigid body
refinement will probably just bias the phases toward "nothing" in the
rest of the asymmetric unit.
I've had correct molrep solutions with R-factors that high, so
there is hope. But depending on how you refined your partial model,
you could have a completely wrong solution with that R-factor as well.
How sure are you that your solution is really correct? If you
take the rigid-body-refined-only model (to minimize phase bias), and
delete something you know should be well-ordered (a fat side chain if
you've got good data, a helix if you've got lousy data), then make an
Fo-Fc map, does it reappear? If not, forget all the statistics and
start over with your searches. If yes, can you see any sign of the
other domains in that map, that solvent modification might help bring
up from the land of noise?
Phoebe Rice
At 02:38 PM 8/13/2007, you wrote:
Hi, ccp4 community,
I am solving my protein (300 aa) structure using molecular
replacement. The space group is P622. There is only one molecule in
the ASU. The protein is supported to have three domains. We have
solved the domain 1 (120aa) structure; therefore we tried to use it
as a model to solve the new structure. MolRep and Phaser can find
the domain 1. We refined the model and the R and Rfree factor was
around 50%. When we used Coot to see the model and map, we found
that the other two domains are missing. In the map, there is a big
'hole' and little extra density (with 6-fold) inside. It is a big
surprise to us. Is there any possibility that R is around 50 if the
other two domains are missing?
Any suggests to figure out what happen to my structure?
Thanks a lot!
Mousheng Wu
---------------------------------------------------------------------------------------------------------------------------
Phoebe A. Rice
Assoc. Prof., Dept. of Biochemistry & Molecular Biology
The University of Chicago
phone 773 834 1723
fax 773 702 0439
http://bmb.bsd.uchicago.edu/index.html
http://www.nasa.gov/mission_pages/cassini/multimedia/pia06064.html
