<div dir="ltr"><div class="gmail_extra">On Thu, Nov 7, 2013 at 8:34 AM, Zhihong Yu <span dir="ltr"><<a href="mailto:nkyuzhih@gmail.com" target="_blank">nkyuzhih@gmail.com</a>></span> wrote:<br><div class="gmail_quote">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><font color="#000000" size="3" face="宋体">
</font><p style="margin:0in 0in 10pt" class="MsoNormal"><span style="font-family:Calibri;color:rgb(0,0,0);font-size:medium">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?</span></p></div></blockquote><div style><br></div><div style>No, that's a classic example of model bias. Positive (and continuous) mFo-DFc density outside of the placed atoms is what you should be looking for, but I suspect there will be very little. It's basically impossible to tell from this result whether the placement of structureX is even correct, although the Phaser statistics may be informative.</div>
<div style><br></div><div style>One unrelated suggestion: given the low sequence identity, I think it will be very important to properly prepare the input model (use Sculptor for this).</div><div style><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr"><p style="margin:0in 0in 10pt" class="MsoNormal"><span style="font-family:Calibri;color:rgb(0,0,0);font-size:medium">2. If it’s possible, what’s the general optimal procedure I
should follow?</span></p></div></blockquote><div><br></div><div style>I confess I haven't had to solve a structure like this myself - just seen a bunch of datasets where similar attempts didn't work - but it's hard to see how it can be solved without experimental phasing information (SeMet, etc.). The good news is that if you can get a correct MR solution for domainB, you can use MR-SAD to find heavy atom sites and solve the structure, which should be easier than starting from no phases at all.</div>
<div style><br></div><div style>-Nat</div></div></div></div>