Apply anyway, and write a cover letter.
At my university we have a very active cancer drug discovery group, funded by Cancer Research UK. The head of the group had a 3rd (I say "had" becuase he passed away recently, but he managed the group for 15 years). One postdoc has a third, two of the PhD students have 2.2s and the others, 2.1s. No-one has a first, and yet this group is very successful, and their discoveries have made the national press on more than one occasion.
The leader of the group has a firm conviction that imagination and effort are more important in research than the ability to to pass exams: hence the willingness to take on people with less than stellar grades.