I am trying to resist answering ccp4bb ... but > Thanks to all who responded. 180 degrees flip of the problematic NAGs, > did help. If you have a poor density (which I guess, generally is the > case for large glycoprotein structures) you have to depend on trial > and error strategy to get the right NAG conformation. I don't know > how other refinement programs handle this, but after Phenix.refinement > run, one has to definitely check the geometry of the NAGs carefully.
There is no such thing as 'trial-and-error' Look up the polysaccharide you are expecting to find for the species you are working with see for example Varki A et al. Essentials of Glycobiology. Cold Spring Harbor Laboratory Press; 2nd edition http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=glyco2 Note fundamentally that an Asn-Nag is always beta- so why not check in the first place that you have NAG attached in a beta conformation if you have alpha - then you are wrong and the density will flatten the C1 - The ccp4bb notes about rotating 180deg is misleading as it is not a conformational change it is a configurational change. It is made by an enzyme not by a crystallographer - all chemistry in biology is run by enzymes each species makes particular sugars in a particular order look it up, you cant get a oligosaccharide that cant be made by a particular species You are not going to find an N-linked Glycan unknown to glycobiology so first of all look up what is expected e.g. http://www.glycoforum.gr.jp/ http://www.genome.jp/ligand/kcam/ http://www.functionalglycomics.org/static/index.shtml http://www.glyco.ac.ru/bcsdb3/ http://www.casper.organ.su.se/ECODAB/ http://www.functionalglycomics.org/static/gt/gtdb.shtml http://akashia.sci.hokudai.ac.jp/ http://hexose.chem.ku.edu/sugar.php http://www.eurocarbdb.org/ then try http://www.glycosciences.de/modeling/sweet2/doc/index.php this will give you a 3D model in PDB format of your maximum glycan - dont do what has happened in the past in the PDB just try adding sugars at random connections and configurations you can also look at http://www.ebi.ac.uk/eurocarb/gwb/builder.action There are tools on http://www.glycosciences.de/ e.g. http://www.glycosciences.de/modeling/glycomapsdb/ to tell you the expected conformational maps of the glycosidic linkage - you believe in Ramachandran for peptide bonds so why not for glycosidic bonds) The PDB has a legacy of wrong connections, wrong conformations, poor geometry of oligosaccharides especially glycans where the coordinates respresent unknown molecules The density may be poor but if you know what say a plant may produce then fit what you can of that particular saccharide in observable density the linkages, 1-2, 1-3, 1-4, 1-6 are all specified and people should stop making them up at random for example plants have basically these N-glycans http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=glyco2&part=ch22&rendertype=figure&id=ch22.f1 sweet (above) will make the 3d coordinates you can try fitting as much as is observed knowing the configuration and trying the conformations from glycomapsdb