Dear Sun,
I had a similar problem. If you have a good TaBr dataset this should
give you good phases.
You can combine the TaBr phases and Molrepl phases in SHARP.
What worked in my hands very well and is easy to do: SAD using Phaser
and the partial Mol Repl Model.
You find here a input file for such a scenario:
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Phenix#phenix.phaser_-_SAD_phasing_with_Phaser
Or simply use the CCP4 gui Phaser and 'SAD with molecular replacement
partial structure'
After DM or parrot you might get some interpretable density even at 6.5 A.
If you don't have a good Mol Repl Model for the missing part you might
try http://toolkit.tuebingen.mpg.de/hhpred
to look for structures that are not that closely related.
SeMet can help a lot in this case too. You will get the SeMet positions
at low resolution with Phaser as described above.
The SeMet positions will guide you to place a model into a very crude
density.
HTH,
Guenter
Dear Crystallographers,
I'm working on a ~90KDa membrane protein, with big extracellular part,
probably function as dimer.
Now we have dataset to ~4.2 Angstrom and using extracellular homolog
structure we can find a solution for this part(~45% of the whole
molecule MW) through molecular replacement, and the molecules are
packed as layers, and the other part are presumably between these
layers. However, we are having trouble to fit the rest of the protein
even though there're some density between the solved part. Rfree is at
40% now.
We're trying to do heavy atom soaking, such as TaBr. We collected data
for MIR but it's not helping so far. (Can I combine these MIR data
with the native dataset because the MIR set is only at ~6.5 Angstrom)?
Other information: this protein is expressed in Sf9 cells (so very
hard to do Se-Met derivatives). The crystals is nice and big and cubic.
Any suggestions or examples? Thanks a lot.
Bingfa
