Hi AA,
On 1 Oct 2008, at 20:34, AA wrote:
Hello everyone,
Please forgive my ignorance about the field of crystallography. I have
recently started to process the diffraction data of a protein with a
ligand
attached to it. we have the structure of this protein already known
and also
known with different ligands. the way I did it is as flllows:
I process the images in mosflm and then integrate them using scala
inccp4i.
After that I do molecular replacement by phaser. and finally refine
it using
refmac. Am I doing it correctly?
Yes that is correct but don't stop here.
Now since I am completely new to all this, I have not much clue
about the
outputs I get and if they are correct or not. What are the key
things you
should be looking at in the log files generated by phaser and
refmac? Till
now I get overall R factor of 29.32 and Rfree of 34.94.
this is a solid indication that the MR actually worked - as you would
expect as you already know the structure.
Is this fine or can
I improve it more?
You should next use the program Refmac and refine your molecular
replacement solution to your highest resolution dataset you have.
If yes then what do I do to further improve the
statistics?
As a rule of thumb multiply the highest resolution limit to which your
data was processed/collected by the factor of ten this or better is
what you are aiming for with the Rfactor, the gap between Rwork and
Rfree should not exceed 5% e.g. Rfactor =25 and Rfree<=30
What should be the RmsBond and Rms Angle values? Since the
structure is already solved a number of times with different
ligands, what
final values should i aim for to get a decent density maps in which
I can
fit my ligand structure.
Sorry for being so naive. Any sort of information or papers or links
would
be very helpful.
Do you have someone at your university who you could bug directly ?
It's much easier to learn from someone with experience than to read
something.
Good luck !
Jürgen
Thanks a lot.
AA
-
Jürgen Bosch
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
Web: http://faculty.washington.edu/jbosch
