Allow only pdf documents on upload

change-allowed-media-types-document.php

<?php

/**
 * Allow only pdf documents on upload.
 *
 * Only allow documents which has pdf extension.
 *
 * @param array $allowed_types Allowed types of media to upload.
 *
 * @return array Allowed types of media to upload
 */
function tmp_rtm_change_allowed_types_documents( $allowed_types ) {
	if ( isset( $allowed_types['document'], $allowed_types['document']['extn'] ) ) {
		// change allowed document type to pdf only.
		$allowed_types['document']['extn'] = array( 'pdf' );
	}
	return $allowed_types;
}
add_filter( 'rtmedia_allowed_types', 'tmp_rtm_change_allowed_types_documents', 999, 1 );

Place this code snippet in a php file in mu-plugins folder of your site