I have seen proteins refined as 'the same', modeled to an averaged map etc only to have one of them with much higher Bj because most likely they are NOT the same so watch out by treating them as 'the same' you are losing the very valuable information that you might be looking for
Ewa ******************************************************** Dr Ewa Skrzypczak-Jankun Associate Professor University of Toledo Office: Dowling Hall r.2257 Health Science Campus Phone: 419-383-5414 Urology Department Mail Stop #1091 Fax: 419-383-3785 3000 Arlington Ave. e-mail: ewa.skrzypczak-jan...@utoledo.edu <mailto:ewa.skrzypczak-jan...@utoledo.edu> Toledo OH 43614-2598 web: http://golemxiv.dh.meduohio.edu/~ewa <http://golemxiv.dh.meduohio.edu/~ewa> ******************************************************** ________________________________ From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Jim Fairman Sent: Tuesday, March 24, 2009 11:25 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] two identical proteins in one asymmetric unit Sang Hoon, Each molecule in the asymmetric unit is most likely different. I work on a protein that crystallizes as a homodimer with 2 molecules per asymmetric unit and there are some differences between the two (eg: electron density visible for the 14 N-terminal residues in one molecule, but not the other). Cheers, Jim On Tue, Mar 24, 2009 at 11:03 AM, Folmer Fredslund <folm...@gmail.com> wrote: Dear Sang They are really different! And I guess you would probably want to use NCS restraints depending on your resolution. Regards, Folmer 2009/3/24 Sang Hoon Joo <s...@duke.edu>: > I am refining my crystal structure in which I have two identical > chains in one asymmetric unit. > Space group is H32 and each chain yields me a biological trimer as expected. > The problem is, do I have to assume they are identical, or they are > really different. > After each cycle of refinement, if I try to align two molecules I get > ~ 0.17 RMSD. > -- > Sang Hoon Joo, PhD > Postdoctoral Associate > Duke University > 239 Nanaline H. Duke > Box 3711, DUMC > Durham, NC 27710 > -- Jim Fairman Graduate Research Assistant Department of Biochemistry, Cellular, and Molecular Biology (BCMB) University of Tennessee -- Knoxville 216-368-3337 jfair...@utk.edu james.fair...@case.edu
