I'll address NMR for structure determination. It is the less common method, only ~10% of protein structures are determined this way, though it has e.g. advantages for nucleic acids and more than a third of those was solved by NMR. Take any numbers here as very rough estimates, there are a lot of factors that influence the difficulty and cost.
For NMR, the single most important factor is size. A stable, well-behaved protein of 10-20 kD is pretty much routine. Large proteins are either very difficult to measure or outright impossible by NMR.
You need large quantities of protein for X-ray and NMR, but in the case of NMR you also need it isotope-labeled. Uniformly labelling proteins 15N/13C isn't all that expensive if you can express your protein in E. coli in minimal medium (around $100 per liter medium or so, mostly in 13C glucose), but it can get really expensive very fast if you need full medium or anything fancy.
Your protein needs to be stable in solution for a few days at least, a single 3D experiment can take multiple days to measure. If your protein is barely stable enough, you also have to produce much more protein because you need to use many samples to perform all necessary experiments. A complication here is that you can't add a lot of salt to an NMR sample without drastically reducing the sensitivity of the NMR experiments. But some proteins are hard to get stable in a low-salt environment.
You need something like a few weeks of measurement time on a high-field NMR spectrometer, though this depends a lot on the size of the protein and the concentration you can achieve in your sample and the general difficulty of assigning the protein resonances. This kind of spectrometer can cost a few millions, and you need to supply liquid nitrogen and liquid helium to keep them working. Something like a $1000 per day measurement time is a number I've heard about the cost, but there are a lot of factors that go into this and I can't say how accurate this number is.
Then you need to assign the resonances in your protein, which takes a single person several months. This again varies a lot depending on the difficulty.
Then you need to calculate the structure, and typically this requires several rounds of refining the assignment and analysis and redoing the calculations. It's not really expensive in terms of computer power, but it takes quite some work by the person running the calculations and checking them.