<div dir="ltr">How do the rest of the intensity statistics look?<div><br></div><div>P</div></div><div class="gmail_extra"><br><div class="gmail_quote">On 10 July 2015 at 14:41, John Bruning <span dir="ltr"><<a href="mailto:jmbruning@gmail.com" target="_blank">jmbruning@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div class="gmail_default" style="font-family:'arial black',sans-serif;font-size:small;color:rgb(68,68,68)"><div class="gmail_default" style="color:rgb(34,34,34);font-family:arial,sans-serif"><font face="arial black, sans-serif" color="#444444">Hi Everyone,</font></div><div class="gmail_default" style="color:rgb(34,34,34);font-family:arial,sans-serif"><font face="arial black, sans-serif" color="#444444">I collected two datasets of the same ligand bound structure at 2.4 and 2.1 Å resolution. The apo structure has already been solved to 2.2Å resolution in P31 (and P3121 for SeMet). After processing each dataset as both P31 and P3121 in MOSFLM, I proceeded with MR with Phaser using sequential partial search models to place either 3 copies in the ASU for P3121, or 6 copies for P31. (The previously solved apo structure had 6 copies of the same protein in the ASU). </font></div><div class="gmail_default" style="color:rgb(34,34,34);font-family:arial,sans-serif"><font face="arial black, sans-serif" color="#444444">*** in summary two datasets, processed as both P31 or P3121 </font></div><div class="gmail_default" style="color:rgb(34,34,34);font-family:arial,sans-serif"><font face="arial black, sans-serif" color="#444444"><br></font></div><div class="gmail_default" style="color:rgb(34,34,34);font-family:arial,sans-serif"><font face="arial black, sans-serif" color="#444444">After running xtraige for either .mtz, I get this warning about NCS:</font></div><div class="gmail_default" style="color:rgb(34,34,34);font-family:arial,sans-serif"><p><font face="arial black, sans-serif" color="#ff0000">Largest Patterson peak with length larger than 15 Angstrom:<br> Frac. coord. : 0.333 -0.333 -0.153<br> Distance to origin : 56.728<br> Height relative to origin : 26.388 %<br> p_value(height) : 2.659e-03symmetry.</font></p><p><font face="arial black, sans-serif" color="#ff0000">Translational pseudo-symmetry is very likely present in these data. Be aware that this will change the intensity statistics and may impact subsequent analyses, and in practice may lead to higher R-factors in refinement.</font></p></div><div style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:12.8000001907349px"><div class="gmail_default" style="font-size:small"><font face="arial black, sans-serif" color="#444444">Regardless, I can proceed with the MR using sequential partial search models to place either 3 copies (P3121) or 6 copies (P31) with decent solutions (i.e. packing looks good upon inspection, scoring looks appropriate -> SOLU SET RFZ=2.8 TFZ=8.3 PAK=13<b>LLG</b>=-37 <b>LLG</b>=2199 as an example). However, I did get the following somewhat expected warnings:</font></div><div class="gmail_default" style="font-size:small"><p><font face="arial black, sans-serif" color="#ff0000">Number of known components (1) not divisible by 2: Translational <b>NCS</b> correction not applied<br>Large non-origin Patterson peak indicates that translational <b>NCS</b> is present</font></p></div><div class="gmail_default" style="font-size:small"><span style="color:rgb(68,68,68);font-family:'arial black',sans-serif">Upon any attempt at initial refinement (with a number of different strategies), the R-factors are hung up > 0.42 (for example in the P3121, 2.1Å case):</span><br></div><div class="gmail_default" style="font-size:small"><font face="arial black, sans-serif" color="#444444">Start R-work = 0.4966, R-free = 0.5133<br>Final R-work = 0.4231, R-free = 0.4477</font></div><div class="gmail_default" style="font-size:small"><font face="arial black, sans-serif" color="#444444">*** best R-factors from ~ 15 different strategies</font></div><div class="gmail_default" style="font-size:small"><font face="arial black, sans-serif" color="#444444"><br></font></div><div class="gmail_default" style="font-size:small"><font color="#444444" face="arial black, sans-serif">My concern is that there is some pathology that is not being recognized (merohedral twinning) or that the NCS/pseudosymmetry is not being addressed appropriately. Any suggestions in troubleshooting this would be much appreciated, as I have pretty much exhausted everything I could think of. </font></div></div></div><span class="HOEnZb"><font color="#888888"><div><br></div>-- <br><div><div dir="ltr"><font face="arial black, sans-serif" color="#444444"> Cheers,<br> John</font><br></div></div>
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Unsubscribe: <a href="mailto:phenixbb-leave@phenix-online.org">phenixbb-leave@phenix-online.org</a><br></blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div>-----------------------------------------------------------------<br>P.H. Zwart<br>Staff Scientist<br>Berkeley Center for Structural Biology, Science lead<br>Lawrence Berkeley National Laboratories<br>1 Cyclotron Road, Berkeley, CA-94703, USA<br>Cell: 510 289 9246<br>SASTBX: <a href="http://sastbx.als.lbl.gov" target="_blank">http://sastbx.als.lbl.gov</a></div><div>BCSB: <a href="http://bcsb.als.lbl.gov" target="_blank">http://bcsb.als.lbl.gov</a><br></div><div>PHENIX: <a href="http://www.phenix-online.org" target="_blank">http://www.phenix-online.org</a></div><div>CAMERA: <a href="http://camera.lbl.gov/" target="_blank">http://camera.lbl.gov/</a></div><div>-----------------------------------------------------------------</div></div></div></div></div>
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