Hello,
In continuation to my earlier thread (subject: sequence
independent model building possible?), I have built model into
density without knowledge of sequence for a data diffracted to
1.9A resolution. Current R/Rfree is 15/19, phaser error=16.88
degrees with no Ramachandran outliers.
Is there a way we can differentiate between Glu/Gln,
Asp/Asn and sometimes Thr/Val directly from density? I have
considered the local environment
(hydrophobic/hydrophilic/polarity pockets, possible hydrogen
bonds/other interactions, buried/exposed, etc...) in choosing
one over the other confusing pairs of amino acids. However, I
am not absolutely certain in many places.
A BLAST of this sequence against all non-redundant protein
sequence database yield highest hit of 80% sequence identity.
Hence, we are still not sure of sequence of the contaminant
protein which got crystallised and want to decipher sequence
directly from the structure.
Thanks for any pointers/suggestions,
Regards,
Kaushik
--
Stupidity is everyone’s
birthright. However, only the learned exercise it!
--Kaushik (28Oct2014)