<div dir="ltr">There is no significant peaks for translational NCS. I also didn't see anything in the patterson map.<div><br></div><div>However, the Multivariate Z score L-test gives 6.218. Also the observed Centric reflections are more intense than they should be but I don't suspect twinning in a monoclinic space group.</div>
<div><br></div><div>-Yarrow</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Thu, Apr 17, 2014 at 4:37 PM, Paul Adams <span dir="ltr"><<a href="mailto:pdadams@lbl.gov" target="_blank">pdadams@lbl.gov</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"><br><div>What does triage say about translation NCS? </div></div><div class="gmail_extra"><br><br><div class="gmail_quote">
<div><div class="h5">On Thu, Apr 17, 2014 at 4:25 PM, Yarrow Madrona <span dir="ltr"><<a href="mailto:amadrona@uci.edu" target="_blank">amadrona@uci.edu</a>></span> wrote:<br>
</div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5"><div dir="ltr">Hello,<div><br></div><div>I using the latest stable build of phenx.refine (1.8.4) I recently collected data, processed and obtained an MR solution using phaser. I am stuck trying to refine with an Rfree sitting at 40%</div>
<div><br></div><div>I really want to know if the high Rfree is due to poor data quality or if non-crystallographic symmetry involving a near perfect two fold rotation between the two molecules in the ASU could somehow impede refinement. Stats and other information is below. Thank you for any help you can give.</div>
<div><br></div><div>-Yarrow</div><div><br></div><div><br></div><div>Visually, the quality of the data is marginal at best (streaky/ice rings in many frames) despite good processing stats from XDS. Processing with mosflm or HKL2000 managed to index but failed pretty bad in integration and scaling.</div>
<div><br></div><div>Phaser gave high TFZ scores for 2 molecules in the asu (see below).</div><div><br></div><div>Density for a cholesterol like ligand shows up even though not present in the search model. </div><div><br>
</div>
<div>MolRep Self rotation shows rotational symmetry. </div><div><a href="https://www.dropbox.com/s/2zsajl5o091k50r/CYP142A2-032814_21_rf%20copy.pdf" target="_blank">https://www.dropbox.com/s/2zsajl5o091k50r/CYP142A2-032814_21_rf%20copy.pdf</a></div>
<div><br></div><div>The 2 molecules in the ASU are related by almost a 2 fold rotation:</div><div><br></div><div><div>Rotation matrix for chain A to chain B:</div><div><br></div><div>new_ncs_group</div><div>rota_matrix 1.0000 0.0000 0.0000</div>
<div>rota_matrix 0.0000 1.0000 0.0000</div><div>rota_matrix 0.0000 0.0000 1.0000</div><div>tran_orth 0.0000 0.0000 0.0000</div><div><br></div><div>center_orth 15.2016 0.5245 33.7070</div>
<div><br></div><div>rota_matrix -0.9860 -0.1636 -0.0309</div><div>rota_matrix -0.1659 0.9511 0.2605</div><div>rota_matrix -0.0132 0.2620 -0.9650</div><div>tran_orth 34.3310 -24.0033 107.0457</div>
<div><br></div><div>center_orth 15.7607 7.2426 77.7512</div></div><div><br></div><div><div>RMSD, B onto A = 0.0007 after phaser</div><div>RMSD, B onto A = 0.347 after one round of refinement in phenix</div></div><div>
<br></div><div><br></div><div>Refinement using aniostropically corrected data (ucla web server: <a href="http://Services.mbi.ucla.edu/anisoscale" target="_blank">Services.mbi.ucla.edu/anisoscale</a>) did not improve the Rfree in refinement.<br>
</div><div><br></div><div><br></div><div>Statistics are listed below:<br></div><div><br></div><div>UNIT CELL: 51.487 88.923 89.592 90 97.15 90 P21<br></div><div><br></div><div><div>RESOLUTION NUMBER OF REFLECTIONS COMPLETENESS R-FACTOR R-FACTOR COMPARED I/SIGMA R-meas CC(1/2) Anomal SigAno Nano</div>
<div> LIMIT OBSERVED UNIQUE POSSIBLE OF DATA observed expected Corr</div><div><br></div><div> 5.99 8280 1927 2087 92.3% 3.1% 3.3% 8246 35.09 3.5% 99.8* 20* 0.909 1296</div>
<div> 4.30 14606 3401 3487 97.5% 3.3% 3.5% 14580 33.37 3.8% 99.9* 11* 0.843 2273</div><div> 3.53 17961 4244 4445 95.5% 3.8% 3.9% 17944 31.11 4.4% 99.8* -2 0.789 2721</div>
<div> 3.06 21954 5068 5221 97.1% 4.9% 5.1% 21933 24.81 5.6% 99.7* -2 0.780 3455</div><div> 2.74 25741 5830 5933 98.3% 7.6% 7.6% 25713 18.88 8.6% 99.5* -2 0.782 4165</div>
<div> 2.51 27859 6311 6483 97.3% 10.8% 10.8% 27824 14.06 12.3% 99.1* -2 0.774 4385</div><div> 2.32 31336 6979 7084 98.5% 14.9% 15.3% 31296 10.49 16.8% 98.5* -4 0.748 5095</div>
<div> 2.17 32396 7347 7567 97.1% 22.3% 22.7% 32341 7.46 25.4% 97.3* -7 0.728 5055</div><div> 2.05 32254 7339 8047 91.2% 33.1% 33.5% 32075 5.06 37.5% 94.8* -6 0.724 5155</div>
<div> total 212387 48446 50354 96.2% 7.8% 7.9% 211952 16.57 8.8% 99.7* -3 0.768 33600</div></div><div><br></div><div>Processing with mosflm or HKL2000 managed to index but failed pretty bad in integration and scaling.</div>
<div><br></div><div><br></div><div>Phaser:</div><div><br></div><div>SOLU SET RFZ=27.5 TFZ=24.2 PAK=0 LLG=1711 RF++ TFZ=64.6 PAK=0 LLG=3610 LLG=4865<br></div><div><br></div></div>
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<br></blockquote></div><br><br clear="all"><div><br></div>-- <br><div style="color:rgb(34,34,34);font-size:12px;font-family:Helvetica">Paul Adams<br>Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab<br>
Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab</div><div style="color:rgb(34,34,34);font-size:12px;font-family:Helvetica">Adjunct Professor, Department of Bioengineering, U.C. Berkeley<br>
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