[phenixbb] C-C sugar linkage in real-space refinement

Kevin Jude kjude at stanford.edu
Mon Jun 14 00:31:37 PDT 2021

I'm trying to refine a cryoEM structure that contains some MAN/C1-TRP/CD1
glycosylations. I've done this successfully in crystallographic reciprocal
space refinement, using cif files to define the MAN geometry and the
MAN-TRP linkage, plus adding LINK instructions to the pdb file. In this
cryoEM structure, though, using the same .cif definition files and similar
LINK instruction, the bond is still not defined in the .geo file and
instead it's treated as a nonbonded interaction, kicking the mannose away
from the indole side chain. The NAG-ASN linkages in the cryoEM structure
are fine. Do I need to do anything differently to define these linkages in
Real Space Refine compared to phenix.refine?

Kevin Jude, PhD (he/him/his)
Structural Biology Research Specialist, Garcia Lab
Howard Hughes Medical Institute
Stanford University School of Medicine
Beckman B177, 279 Campus Drive, Stanford CA 94305
Phone: (650) 723-6431
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