beta sheets in really well-phased low-resolution maps should look sort of like walls, but in an imperfect map they might by rather spotty.
I'd be very leary of making any conclusions from molecular replacement at such low resolution. For a good control, try "solving" your data set with a similar-sized but completely different protein as the search model, and see what kind of statistics and map you can get for something you know is garbage. Can you get experimental phases or SeMet data that will at least verify the position of your model? Phoebe ===================================== Phoebe A. Rice 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 http://www.rsc.org/shop/books/2008/9780854042722.asp ---- Original message ---- >Date: Fri, 12 Aug 2011 13:32:00 -0400 >From: CCP4 bulletin board <[email protected]> (on behalf of Huiming Li ><[email protected]>) >Subject: [ccp4bb] consistently missing eletron density >To: [email protected] > > Dear All, > > I am working on a structure using several sets of > data collected between 5 to 6 angstroms. I have > never worked with such low resolution before. I was > able to get pretty good TFZ between 10 and 16, and > the electron density looks overall pretty good. > However, among the three data sets I have processed > so far, a large chunk of density is missing in all > of them around the same area of the protein (largely > beta sheet). Is this a manifestation of some > intrinsic problems of the crystal, the data, or the > protein? Is there a proper procedure I can take to > get this density back to make the map a bit more > pleasing to view? > > Thanks, > > Huiming Li, Ph.D. > Immune Disease Institute > Children's Hospital Boston
