I have a protein that got recently diffracted at 1.9A. I am unable to do molecular replacement since my template model is from P3 spacegroup. There is greater than 90% similarity between my protein and the template. Is there any way to solve the structure? I tried Molrep, Phaser, Autobuild, Refmac, with no improvement from either of them. Please suggest me a way to do molecular replacement.
Thanks,
Immanuel.
Are you performing molecular replacement with a monomer/single chain? If so, the difference in space group shouldn't matter as the software should perform molecular replacement in the correct space group.
I would try removing the loops from the protein and keep only helices and sheets, since flexible regions may affect the packing and create crashes in a crystal form different from the original.
Are there multiple domains in your protein? Sometimes, different domains may move relative to each other. Try doing molecular replacement by inputting each domain separately, or try using only the largest domain.
One time, I tried molecular replacement and it didn't work. I solved the structure with selenomet derivative, and the 3D structures were very similar indeed. Sometimes, molecular replacement can be a pain even with a very close model.
If you still can't solve the phases with molecular replacement, I would consider experimental methods, such as growing selenomet form of your protein. If that is too much effort for you, try halide soaks.
I agree with Arthur. There are still some things you can do such trying Balbes, MrBump and Ample. Also reprocessing your data very conservatively sometimes works. There is a small risk that you have a different protein than you expect, this is where experimental phasing really is needed.
Thank you Robbie and Arthur. yes, I performed MR with single chain. It does look like I need to make either selenomethione replaced crystals or improve crystals that belong to other space group. I tried Balbes and Mr.Bump. It didn't work either. Thank you for your suggestions :)
I just had the same kind of problem recently and it turned out that the true space group was I2 (with alph=beta=gamma=90°!) instead of I222. I would recommand you to test MR with this space group. Also I would recommand you to try aimless (in CCP4) to determine your space group.
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