<div class="gmail_quote"><font face="'Times New Roman'"><p class="MsoNormal">Hello everyone,</p><p class="MsoNormal">
<br></p><p class="MsoNormal">I have a few crystals to be x-rayed next week. Before that I hope to get a clear idea about what I am doing (I am new to anomalous scattering). </p><p class="MsoNormal"><br></p><p class="MsoNormal">
Facts:</p><p class="MsoNormal"></p><ol><li>The crystal is a protein co-crystallized with a ligand</li><li>The protein structure is known.</li><li>The ligand has a heavy atom bromide (absorption K-egde=13.47Kev)</li><li>Data resolution is ~3 angstrom</li>
</ol><p></p><p class="MsoNormal"><br></p><p class="MsoNormal">Goals:</p><p class="MsoNormal"></p><ol><li>Locate the bromide position</li><li>Locate and refine the ligand</li></ol><p></p><p class="MsoNormal"><br></p><p class="MsoNormal">
Questions:</p><p class="MsoNormal"></p><ol><li>Do I need to carry out MAD experiment at 3 wavelengths or there is some other easier way since the protein structure is known (I am not expecting big change of the protein structure itself)?</li>
<li>Assuming I have the MAD data, what should I do next using phenix to achieve the two goals listed above? Here are some thoughts:</li><ul><li>Using phenix.hyss to locate the anomalous scatterers </li><li>Using phenix.autobuild to build the protein model (which data set to use?)</li>
<li>Using coot to add ligands to the protein structure (Is the relative position between the protein and the ligand known based on phenix.hyss and phenix.autobuild?)</li><li>Using phenix.refine to refine the ligand+protein complex</li>
</ul></ol><p></p></font><p></p><p class="MsoNormal"><font face="'Times New Roman'"></font></p><font face="'Times New Roman'"><p class="MsoNormal"><br></p><p class="MsoNormal">
Thank you all for reading this.</p><p class="MsoNormal"><br></p><p class="MsoNormal"><span class="Apple-style-span" style="font-family: arial; "> </span></p></font></div><div>======================</div>Jason<div>Structural Biology Department</div>
<div>University of Pittsburgh</div><div>======================</div><br>