1 What is the expected Rfree and Rwork for such low resolution data? I looked up PDB bank, and there is a 11.5A crystal with Rfree=~0.4. But not sure whether there is a kind of value for Rfree to consider the refinement works or not. It's difficult to come up with any meaningful statistics, because these structures are usually barely refined, for obvious reasons. (R-free in the high 30s is not uncommon for published structures, however.) I don't understand the math well enough to know what to expect, but I've seen R-factors in the mid-to-low 40s for structures refined against nonsense low-resolution data (again ~6Å). An R-free of 0.49 is very suspicious.
It can be anything, and low too. Just take any known structure, cut data at 15A and compute R, you may get 10% for well placed molecules. This and references therein may help to set expectations: http://journals.iucr.org/d/issues/2012/06/00/wd5173/index.html Pavel