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My suggestion would be to refine with full glu and then put either O and C atoms at the region corresponidng to the extra electron density..... On Wed, May 18, 2011 at 1:41 PM, Borhani, David < [log in to unmask]> wrote: > Glutamate methyl ester? (or ethyl ester, which I’m not sure has ever been > documented…hard to tell how many extra heavy atoms given the view direction > in the image you supplied). Or the methyl/ethyl amides. > > > > Dave > > > > *From:* CCP4 bulletin board [mailto:[log in to unmask]] *On Behalf Of *Bosch, > Juergen > *Sent:* Wednesday, 18 May 2011 14:06 > *To:* [log in to unmask] > *Subject:* Re: [ccp4bb] unknown density > > > > I take the lysine back, just realized wrong color coding it's an oxygen and > not a nitrogen closer to the extra density :-) > > Jürgen > > > > On May 18, 2011, at 2:03 PM, Bosch, Juergen wrote: > > > > But that's a lysine, so maybe a PTM ? Acetylated perhaps ? > > > > Jürgen > > > > On May 18, 2011, at 1:56 PM, Shiva Bhowmik wrote: > > > > Hi Cedric, > > > > I presume you collected the datset at a synchrtron source. It could be free > radical generated due to X-ray radiation has modified the glutamate > residues. I have seen this happening for Ser residues. > > > > Cheers, > > > > Shiva > > On Wed, May 18, 2011 at 9:08 AM, cedric bauvois <[log in to unmask]> > wrote: > > Hi, everyone, > > I am working on the refinement of a structure at about 1.4 Ang and found > some clear extra density connected to a glutamate (see figure), but I don't > know what it should be. The crystal came out from Tris-HCl buffer with > peg600, and protein buffer contains sodium-phosphate. > > Does anyone figure out what this density can be ? > Thanks for any help you can give. > > Cédric > > > > > > ...................... > > Jürgen Bosch > > Johns Hopkins Bloomberg School of Public Health > > Department of Biochemistry & Molecular Biology > > Johns Hopkins Malaria Research Institute > > 615 North Wolfe Street, W8708 > > Baltimore, MD 21205 > > Phone: +1-410-614-4742 > > Lab: +1-410-614-4894 > > Fax: +1-410-955-3655 > > http://web.mac.com/bosch_lab/ > > > > > > > > > > ...................... > > Jürgen Bosch > > Johns Hopkins Bloomberg School of Public Health > > Department of Biochemistry & Molecular Biology > > Johns Hopkins Malaria Research Institute > > 615 North Wolfe Street, W8708 > > Baltimore, MD 21205 > > Phone: +1-410-614-4742 > > Lab: +1-410-614-4894 > > Fax: +1-410-955-3655 > > http://web.mac.com/bosch_lab/ > > > > > > >