Dear Mohamed, It happens quite often, that part of a ligand is disordered and not visible in the electron density maps. In this case, I would delete the nicotinamide-ribose part which is not defined in the electron density. Some more remarks:
- it looks to me that the pyrophosphate groups have not been fitted correctly, and that the first phosphate has to go to the position of the two waters, and the second, poorly defined phosphate to the current position of the first phosphate. - What is the function of the NADP, is at a cofactor of an enzyme? In this case it might have been turned over to NADPH and not bind correctly any more. However, due to air oxidation the reaction usually goes from NADPH to NADP. Again, if your protein is an enzyme, is NADP a substrate or a product? If it is a product, it might bind poorly since it has to leave the active site for the reaction to proceed. - You seem to have a decent resolution. I would also refine a few cycles without NCS and see what happens, especially if there are differences between the NCS related monomers. If there are differences, I would model them and drop or relax the NCS. Best, Herman -----Ursprüngliche Nachricht----- Von: CCP4 bulletin board [mailto:[email protected]] Im Auftrag von Mohamed Noor Gesendet: Donnerstag, 25. August 2016 14:21 An: [email protected] Betreff: [ccp4bb] NAP ligand refinement Dear all I have fitted the NAP (NADP) ligand into my model, with the occupancy refined to 0.88. However, the density does not fully cover the entire molecule. Does this happen frequently? How should I model it? In another NCS-related copy, the part of the molecule without density actually clashes with some protein residues. A small attachment is included. The crystals were grown in the presence of NADP+. The data extends to 1.9 A. Thanks. Mohamed
