Dear Joane, we had a case, where we had five molecules in the assymmetric unit where the biological functional unit was a homotrimer. So we had one non-crystallographic trimer and two monomers, which were located along the 3-fold symmetry axis of space group I213. One of the monomers also showed electron density of considerably lower quality, obviously going along with higher B-factors. By a careful analysis of the crystal packing we could see that this chain has only very few crystal contacts.
If you want to have a closer look, see: Schuldt L, Weyand S, Kefala G, Weiss MS J. Mol. Biol. (2009), 863-879. The Section "Crystal Packing and structural variation" describes this in more detail. Best wishes, Linda Joane Kathelen Rustiguel schrieb: > Dear all > > > I am refining a structure at 3.4 A resolution that contains 3 molecules in > the > a.u. The chain A sits on a 2-fold crystallographic axis forming the > dimeric > functional structure expected for this class of proteins. The other two > chains > B and C, which also form the functional dimer, seem to be, somehow, a lot > more > flexible than chain A. As a result, whereas the electron density map, > b-factor > and geometry for chain A is pretty reasonable for a 3.4 A resolution > structure, the refinement for the other two chains (B and C) does not > behave > well. Even playing with different weights for geometry, analysing > different > levels of 2Fo-Fc/Fo-Fc maps, using NCS, TLS, etc..., nothing works. The > map > for the helical regions is ok, but the electron density map for strands > and > loops of chains B and C are broken along the main chain, B-factors are > really > high, and the geometry keeps being distorted. > > Right now, the R-factor and R-free are 24.2 and 28.6, respectively. > > Any suggestions in how to proceed the refinement? > And even a more difficult question, how do we report this type of > structure? > How do we deposit those coordinates? We can certainly use chain A as a > model > to perform interesting studies of structure-function relationship, but we > know > that chain B and chain C have problems. > > Any help will be greatly appreciated. > > Regards > > Joane > > > -- > Joane Kathelen Rustiguel Bonalumi > Faculdade de Ciências Farmacêuticas de Ribeirão Preto - USP > Laboratório de Cristalografia de Proteínas > Departamento de Física e Química > Fone: +55.16.3602.4193 > ******************************* Dr. Linda Schuldt Department of Molecular Biology University of Aarhus Science Park Gustav Wieds Vej 10c DK-8000 Århus C Denmark
