Installing an SSL certificate, the necessary files came in a .zip but apache expects a .ca-bundle, key and crt file. Some of those files have to be combined into one ca-bundle file and configured in the site config.
[Solution]
Three files have to be cat'ed together to get the ca-bundle file:
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cat COMODORSADomainValidationSecureServerCA.crt COMODORSAAddTrustCA.crt AddTrustExternalCARoot.crt > MySite-SSL.ca-bundle
Now configure the site config in /etc/apache2/sites-available/ssl-MySite and add the bundle, key and crt file like this (Apache 2.x syntax):
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SSLCertificateFile /etc/apache2/ssl/MySite-SSL.crt
SSLCertificateKeyFile /etc/apache2/ssl/MySite-SSL.key
SSLCertificateChainFile /etc/apache2/ssl/MySite-SSL.ca-bundle