How hard it is to determine a 3d structure of a protein?
Experimental protein structure determination is hard: the most common method is X-ray crystallography, which can be done in a few months if you are lucky and can take years if you're not. The problem with X-ray crystallography is that you need good protein crystals, and in most cases, proteins don't crystallize very well, so it takes a lot of time (and a lot of purified protein) to get the right crystal. (In the comments section Cody added some good links with more in-depth abut X-ray crystallography for structure determination relating to ATP synthase).

The cost is mainly based on the materials &amp; manpower you need for this, and you need to test a lot of different solutions to crystallize your protein in, which aren't very cheap. If you don't have access to specialised equipment for making the crystals (mostly pipetting robots) or the measurement (X-ray beamline), this is going to be super expensive.

Crystallography requires protein crystals, which are sometimes too troublesome to obtain. Other methods that do not require crystals, such as NMR and cryoEM, are even more difficult to perform though less luck dependent. These techniques rely on very expensive equipment and often cannot resolve the structure as precisely as protein crystallography. So unless you can find one of the few people who have experience with these methods, you'll run into a lot of additional problems.

There is also computational structure prediction, which only needs a powerful computer. However, unless your protein is very similar to one with a known structure it will probably not work reliably. As mentioned in the comments there are web server's for the established methods and progress is constantly made on new(er) algorithms, so depending on your needs it's definitely worth a shot to try computational structure prediction.