I know you can set the protocol/cipher via your web server:
Nginx:
ssl_protocols TLSv1 TLSv1.1 TLSv1.2; ssl_ciphers HIGH:!aNULL:!MD5; Apache:
SSLProtocol all -SSLv2 SSLCipherSuite HIGH:!aNULL:!MD5 But my question is can a SSL Certificate be created to only work with certain protocols?
And can a certificate be created to only work with certain ciphers?
-SSLv3. In addition to the answer (and my comment) below, nothing in the cert can control which SSL/TLS versions; however, an X.509 cert can and usually does use the ExtendedKeyUsage extension (EKU) to limit to SSL/TLS and not email (S/MIME) or vice versa, which is a 'certain' protocol but likely not the 'certain' protocol you wanted.