I have just purchased a PR3 domain off someone. It used to be a full site, but I just want the domain and the site pages are gone now. Will a permanent redirect of the new domain to my own site have any negative effects on my sites search ranking?
It should not have a negative affect unless the site was banned or penalized. How much positive affect it has depends on how authoritative the site is and how related it is to your site.
using 301 permanent redirect is always advisable for redirecting pages from old domain to new one. So if you like to redirect the pages of the site you have purchased to you new domain then there is no harm. It will inturn boost your site credibility but please do take care of relevancy while redirecting.
If the other site is relevant to yours, then you do not need to do anything else besides redirect it. You should be good to go.