To check ssl is installed correctly, run in command line
openssl s_client -debug -connect yourwebsite.comhistory:443
If you are getting any errors, ssl installation is wrong.
Normally you would get the crt from the intermediate CA. convert it to pem
openssl x509 -inform DER -outform PEM -in server.crt -out server.crt.pem
remember to nginx -t before restarting.