[phenixbb] few questions about resolving new structure through MR

Zhihong Yu nkyuzhih at gmail.com
Thu Nov 7 08:34:16 PST 2013

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 for 3
cycyles, 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!

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