Hi Joane, I'm not sure if I understand your description of the structure (chain A forms the dimer? Does it form a dimer with a crystallographically related chain A?) . But anyway, I don't think you need to worry. Your R/Rfree are excellent for this resolution. There's not much you can do about the fact that some molecules in the AU are less ordered; this happens fairly often. As you say, you can use the best ordered chain as a representative model. Refine everything as well as you can and move on I would say.
Bert On 5/19/11 9:02 AM, "Joane Kathelen Rustiguel" <jkrustig...@usp.br> wrote: 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
