Count yourself lucky that you may have a partial solution for your
structure with only 30% identity. The question now is: can you see any
reasonable, traceable electron density for domain A?
Cheers,
_______________________________________
Roger S. Rowlett
Gordon & Dorothy Kline Professor
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346
tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: rrowl...@colgate.edu
On 11/7/2013 11:36 AM, Zhihong Yu wrote:
Hi, all
I'm a rookie in resolving a brand new structure. I have some questions
for my current case and look forward to some suggestions.
Now I’m working on a protein like this:
N-ter(55aa)—domainA(110aa)—linker(30aa)—domainB(150aa)—C-ter(20aa), I
got a diffraction data just to 3.5Å, and there is no complete homology
structure in pdb bank, but only a homology structure (named as
structureX later) for domainB with ~30% sequence identity, so I have
some questions as following:
1. Is it possible to find a resolution through MR approach using
structureX as a search model? Especially considering that the
resolution is only 3.5Å. Currently I just tried once using phaser and
refine the structure, I can get a R/Rfree of 0.45/0.55, and it looks
like most of backbone in the structureX, especially those within helix
or sheet, can be well described by 2Fo-Fc density. Is this primary
result promising or not?
2. If it’s possible, what’s the general optimal procedure I should
follow?
Really thanks for any advice and suggestions!
Zhihong
