Hi all i m trying to solve the structure of a protein crystallized in p41 space group by molecular replacement. it is a hexameric protein. each asymmetric unit have two trimers. i m solving the structure at 3.2A, by applying NCS between the six protomers. present status of refinement is Rfree: 30.60% and Rcryst: 30.30%, with a fairly good steriochemistry. Among the noncrystallographically related molecules i can see no difference in the main chain but considerable differences in the sidechains. At this stage of refinement with strict NCS i m not able to refine the structure further. i m not able to judge weather i should remove the strict NCS and start refining the individual subunit. so, how should one decide when to remove the NCS and start refining the individual subunits.
My second problem related to the NCS is, whenever i remove NCS n start minimizing the pdb obtained after removing NCS, the Rfree start shooting up very rapidly. is it bcoz of larger differences among the NCS related molecule or bcoz of poorly refined structure. pls suggest me what should i do. I am using CNS for refinement. Thanx in advance Vineet Gaur
