Hi, You may have a very high solvent content, with only 1 in the asymmetric unit. There is certainly precedent for that, particularly with poorly diffracting crystals. Does your current model have packing contacts that would hold the crystal together in all 3 dimensions? And you can find the Se atoms for one monomer just fine, but not for the alleged second monomer? If "yes" to both questions, I'd say you're probably fine. Sometimes the ends of DNA do unexpected things to accommodate good crystal packing - for instance, a base may flip out into the solvent so that the next one can stack against its symmetry mate. The flipped base may be too poorly ordered to see, especially in initial maps. At 3A you probably can't be sure which base is which, so I'd try regrowing the crystals with DNAs where some Ts have been substituted with 5-Br-dU. Good luck! Phoebe Rice
---- Original message ---- >Date: Tue, 19 Jan 2010 10:58:29 -0500 >From: Xun Lu <xlun...@gmail.com> >Subject: [ccp4bb] cannot find the other molecule in the asymmetric unit >To: CCP4BB@JISCMAIL.AC.UK > > Hi All, > > The situation is complicated, and > I am a first yesr PHD student. The data is not good > (3A). Another protein in the same family has been > published recently, so that we could use Molecular > Replacement. > > Matthews's Coefficient suggested > that there are two molecules in the asymmetric unit, > however, we could only find one. It fits pretty > well. And, we have a set of SeMet data. The two Se > peaks are exactly on the sulfuers of the two Mets > (that's very convincing, right?) Phaser and CNS gave > us similar solutions. Anyway, then I started to > build, and I found a problem: there's one DNA base > pair missing in the complex (The DNA we used is > longer than the model, so I needed to add back a few > DNA base pairs. I need to add back two base pairs at > each end, so between two symmates I expect electron > density for four base pairs, right? But I only got > density for three. I really couldn't understand.The > only explaination I can come up with is that the DNA > used in crystallography was wrong, but maybe someone > could give me a few other possibilities.) > > We checked the space group again. > Rmerge of P31 didn't seem better than P3121. The > problem of missing density for DNA still exists... > > Maybe I haven't described my > problem clearly... sorry for bottering... Any > suggestion and comment are welcome. Thanks! > > Xun Lu > Department of Molecular and Structral Biochemistry > North Carolina State University Phoebe A. Rice Assoc. Prof., Dept. of Biochemistry & Molecular Biology The University of Chicago phone 773 834 1723 http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123 RNA is really nifty DNA is over fifty We have put them both in one book Please do take a really good look http://www.rsc.org/shop/books/2008/9780854042722.asp
