Double-dipping to add: Calibre recommends not using PDFs as your source format if at all avoidable.

I feel like I should emphasize that it's not just that the format is ill-suited to conversion, but that Calibre's conversion routine for it is particularly poor; I quit using it when I noticed that the output was frequently truncated early.

Better conversion options:

• The Amazon Send to Kindle application's built-in conversion function
• Opening in a PDF reader and copying and pasting into a word processor
• Searching online for key text and seeing if you can find the document on a Web page; or, if you find the PDF online, saving Google's HTML-converted cached copy

All of those could potentially mess up equations and the like, though; so you might just have to deal with it or get a bigger device.