field-collection-create.php

<?php
//assuming $node exists
  $my_collection = entity_create('field_collection_item', array('field_name' => 'field_my_collection'));
  $my_collection->setHostEntity('node', $node);
  $my_collection->field_text_data[LANGUAGE_NONE][0]['value'] = "hello";
  $my_collection->field_term_ref[LANGUAGE_NONE][0]['tid'] = 123;
  $my_collection->field_node_ref[LANGUAGE_NONE][0]['target_id'] = 345;
  $my_collection->save();
  node_save($node);