Sagar, what you see may be model bias unless you calculated these maps without that region of molecule.
Pavel On Wed, May 27, 2015 at 12:03 PM, Sagar De'Biomimic < [email protected]> wrote: > Dear all, > > We have solved a structure of Protein-DNA complex. In an ASU we have two > protein homodimers and two DNA duplexes. Additionally we were able to model > N-terminal region (NTR) missing in the previously reported structure. > > I had modelled poly-alanine chains in the positive density and refined. > These chains were then joined to form NTR. Finally the entire NTR was > refined for occupancies. > > I am doubtful about the validity of modelling of NTR as i had dropped down > sigma levels to as low as 0.8 (as i could not see much of the noise) of > FO-FC and modelled in positive density. After refinment the region shows > the density at 0.5 sigma level of 2FO-FC. I have attached a pdf file > showing snapshots of NTR at 0.4, 0.5, 0.6, 0.7 sigma level of 2FO-FC map. > > I would like to know crystallography community's opinion on validity of > such modelling. > > This NTR region is highly flexible. Main intention of modelling it in such > a weak signal was to complete the model for our Molecular dynamics > studies. > > Additionally we have confirmed with SAXS DATA using Ensemble optimised > modelling (EOM 2.0), the high flexibility and multiple conformations of > this NTR region. > > I would like to know if there is a possibility of having a tool similar to > EOM to model highly flexible regions of a protein in electron Density. As > far as I know xMDFF does better at lower resolutions but fails to model > highly flexible regions such as ours. > > Thank you. > > Regards > > Sagar > > > > -- > Sagar Khavnekar > Project student, > Structural Biology and Molecular Biophysics lab, > UM-DAE Centre for Excellence in Basic Sciences > University of Mumbai, Vidyanagari Campus, Kalina, Santacruz (East) > Mumbai 400098, India. >
