James, That is a highly subjective question. However, given that your average B-factor is 51, a B-factor of ~87 for the loop is not exceptionally high. It is less than twice the average. If your average B was 10 and your loop had a B-factor of 17 what would you think? I would imagine that if you applied TLS the residual isotropic B-factors might seem very reasonable. The real test is the quality of your maps. I always look as simulated omit maps and even RESOLVE solvent-flipped (reduced bias) maps. Others might use Arp-Warp, DM, Bucaneer/Pirate, or SHARP for density modification/phase improvement. What do Fo-Fc maps tell you? Do you have excess electron density? Are the carbonyls and Cb positions visible in the map? Is this a tube of wispy density which could be a polypeptide or just noise?
Mark On Wed, 2009-05-06 at 03:45 -0500, James Stroud wrote: > Hello, > > I have a 2.45 A structure with an average b factor of 50.6. A region I > am particularly interested in has an average b factor of 87. At what > point do I say that the region is "disordered"? Does it come down to > maps? If I have reasonable simulated omit maps but the b factor is 87, > how much confidence can I have about my interpretation of the maps? > > James Yours sincerely, Mark A. White, Ph.D. Assistant Professor, Dept. Biochemistry and Molecular Biology, Manager, Sealy Center for Structural Biology and Molecular Biophysics X-ray Crystallography Laboratory, Basic Science Building, Room 6.660 C University of Texas Medical Branch Galveston, TX 77555-0647 Tel. (409) 747-4747 Cell. (409) 539-9138 Fax. (409) 747-4745 mailto://[email protected] http://xray.utmb.edu http://xray.utmb.edu/~white
