Follow all necessary stept until Startssl gives you the ssl.key

openssl rsa -in ssl.key -out ssl.key

Follow further stepts until Startssl gives you the ssl.crt
Download StartSSL’s root CA and class 1 intermediate server CA certificates:
http://www.startssl.com/certs/ca.pem
http://www.startssl.com/certs/sub.class1.server.ca.pem

Now create a unified certificate:

cat ssl.crt sub.class1.server.ca.pem ca.pem > ssl-unified.crt

Upload the files ssl.key and ssl-unified.crt to the server
Do not forget to chmod 600 ssl.key
In your nginx ssl vhost include:

ssl on;
ssl_certificate /path/to/ssl-unified.crt;
ssl_certificate_key /path/to/ssl.key;