Dear Yogesh, Since your difference density is at the center of a hexamer, you might be looking at the 6-fold average density of one or two fatty acid molecules. Just try to fit one and generate to other 5 equivalent molecules and look if this makes sense.
Otherwise, I agree with Mark that with hardly any 2mFo-dFC density, you may also be looking at an artifact. Best regards, Herman -----Original Message----- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Mark J van Raaij Sent: Monday, November 05, 2012 9:39 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Extra electron density It may just be noise. Notice there there appears to be no electron density, only difference density. Mark J van Raaij Laboratorio M-4 Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 5 Nov 2012, at 01:38, yogesh khandokar wrote: > Dear All > > I am working on an enzyme which involved in fatty acid biosynthesis. We solved the crystal structure of it. Biological unit of this enzyme is Hexamer and showing extra electron density in the center of Hexamer. Wincoot software doesn't recognize this extra electron density as water molecules/ substrate. > > My question is:Is there any way to find the molecules responsible for extra electron density? > > Picture is attached with email. > > Thanks in advance for your comments. > > Regards > -- > Yogesh Khandokar > PhD Student > School of Biomedical Sciences > Charles Sturt University > Wagga Wagga, NSW, > Australia > http://www.csu.edu.au/faculty/science/biomed/ > > <Doc1.doc>
