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Hi Jan, at low occupancy (and I suppose a resolution that does not extend beyond 2.0 A), you have to rely on your restraints. I think the consensus is that the adenine ring should be planar. The pyridine ring of the nicotinamide should be flat if the ring is oxidized (NAD+), and can be distorted when reduced (NADH). Most NAD molecules in the PDB have strict planar restaints in the pyridine ring of the nicotinamide, even when the density clearly shows that they are puckered. Many NAD+ cofactors get converted to NADH during crystallization by the enzyme they bind. Especially PEG can contain a substrates to convert NAD+ into NADH in the crystal. Best regards, Rob Meijers Synchrotron Soleil --- On Thu, 3/19/09, Jan Abendroth <[log in to unmask]> wrote: From: Jan Abendroth <[log in to unmask]> Subject: [ccp4bb] nad woes To: [log in to unmask] Date: Thursday, March 19, 2009, 12:50 AM Hi all, is there any wisdom on NAD out there? I experience some strange behaviour of this common cofactor. With moderately convincing density, probably low occupancy of a cofactor that came along for the ride from E coli, Refmac5.5.0088 pulls the AN6 atom out of the adenine plane. With my own library that puts planar restraints on the adenine ring this seems to be fixed. Coot during real space refinement or regularisation using either the standard or my own dictionary handles the purine ring just fine, however, totally garbles up the nicotineamide. Btw, I use the * nomenclature. Cheers Jan -- Jan Abendroth deCODE biostructures Seattle / Bainbridge Island WA, USA work: JAbendroth_at_decode.is home: Jan.Abendroth_at_gmail.com