<div dir="ltr">On Fri, May 2, 2014 at 3:48 PM, Yuri <span dir="ltr"><<a href="mailto:yuri.pompeu@ufl.edu" target="_blank">yuri.pompeu@ufl.edu</a>></span> wrote:<br><div class="gmail_extra"><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I am trying to solve a structure (to 2.15 Ang). I am pretty sure about one of the domains fold but it only covers residues 26-250 while the whole protein is 470aa.<br>
Could I attempt to use this small part of the protein to phase my data</blockquote><div><br></div><div>probably, if it's actually reasonably close to your target protein, and not something with 25% sequence identity.</div>
<div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">and hopefully start building?<br></blockquote><div><br></div><div>Very difficult. The density modification in AutoBuild will certainly help, but even with higher resolution the maps for these severely incomplete structures are hard to interpret. If it is helical you might have an easier time, because you could try docking in secondary structure - fitting individual residues is unlikely to work. (I suspect this is somewhat dependent on solvent content, but most of the structures I've tried this with were all around 50% or lower.)</div>
<div><br></div><div>Also, if you have reasonably good anomalous signal for endogenous sulfur, this may help you identify the unbuilt Met sites even if the other maps are unclear.</div><div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
ps. Selenomet protein will be expressed soon..</blockquote><div><br></div><div>The good news is that if MR works, the rest of the phasing process should be a breeze once you have (reasonably good) SeMet data. </div><div>
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</div><div>-Nat</div></div></div></div>