<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Ralf and Pavel,<div><br></div><div>Unfortunately, Phenix didn't recognize a disulfide bond should exist between the sulfur atoms of DTT and the side chain sulfur atom of the cysteine residue in question. I position everything well in the Fo-Fc and 2Fo-Fc maps and ensured the two sulfurs were approximately 2.1 A apart. However, after refinement the DTT molecule moved so the two sulfurs in question where nearly 3 A away. Maybe this is because it is a mixed disulfide between a DTT molecule and a side-chain Cys rather then what most programs expect which is a disulfide between two Cys residues. Is it possible I need to define the complete chemical entity as a hetatm (the disulfide linked Cys residue? Is there a way to specify that a covalent bond should exist between the SG atom of the Cys in question and the S atoms of DTT with DTT lying across the crystallographic two-fold given its internal 2-fold symmetry?</div><div><br></div><div>Joe<br><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: 'Lucida Grande'; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: 'Lucida Grande'; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">___________________________________________________________</div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Joseph P. Noel, Ph.D.<br>Investigator, Howard Hughes Medical Institute<br>Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics<br>The Salk Institute for Biological Studies<br>10010 North Torrey Pines Road<br>La Jolla, CA 92037 USA<br><br>Phone: (858) 453-4100 extension 1442<br>Cell: (858) 349-4700<br>Fax: (858) 597-0855<br>E-mail: <a href="mailto:noel@salk.edu">noel@salk.edu</a><br><br>Web Site (Salk): <a href="http://www.salk.edu/faculty/faculty_details.php?id=37">http://www.salk.edu/faculty/faculty_details.php?id=37</a><br>Web Site (HHMI): <a href="http://hhmi.org/research/investigators/noel.html">http://hhmi.org/research/investigators/noel.html</a><br>___________________________________________________________<br></div></span></span>
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