Hello Rex, Just a few biologically-related ideas that may support modeling the planar conformation.
I'm not sure if the protein you're working with has enzymatic activity, but is it possible that the ring strain is indeed real and may be a part of the reaction mechanism? Are any parts of the protein in contact with the flattened ring in such a way that they might be "pushing" or "pulling" the ring into the planar conformation? Best, Mike ----- Original Message ----- From: "Rex Palmer" <rex.pal...@btinternet.com> To: CCP4BB@JISCMAIL.AC.UK Sent: Monday, August 16, 2010 9:44:39 AM GMT -08:00 US/Canada Pacific Subject: [ccp4bb] Lactose refinement We are attempting REFMAC refinement of a protein structure which is complexed with lactose. One of the rings (the one oriented away from the protein) loses the chair conformation which is flagged as a problem by COOT check chiral volumes . Is there anything we can do to restrain the ring as a chair and would this necessarily be a valid move? ie why can't the conformation deviate from the norm? Rex Palmer Birkbeck College -- Michael C. Thompson Graduate Student Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles mi...@chem.ucla.edu
