Dear Asmita, (and all who may be interested) In Gourinath & Himmel et al. Structure 11:1621-1627 (2003), I normalized B-factors of several crystal structures for comparisons, using a simple applications of statistics. Any such analysis must be viewed with caution, of course, because it relies on the assumption that the crystal structures in question were well-refined with little model bias. Otherwise, it may be useful set all B-factors in a structure to one value (well below the average B, since B-factors tend to refine up much more easily than refining down) and run through a round of refinement in which B-factors are the last parameter refined. Then, normalize and do the comparison.
In my case, I looking at how the difference between B-factors of one particular helix (the "SH1 Helix") and the whole structure changed over several different conformations of the protein, and I had to look at a variety of crystal structures to do the comparison and demonstrate a possible trend. I hope this helps. -Daniel M. Himmel
