Explanation for misuse of 'where' in a main clause
This is correct. Some may prefer the form ", where..." but this has become common form because most word processing software will automatically capitalize the fragment.
To explain why this is correct, you have to consider that someone who knows how to read the equation will read it, followed by the fragment, as a single sentence.
For example:
"E (energy) equals MC squared, where M is the mass in question and C is the speed of light."