<?php

add_action( 'meta_boxes', 'do_my_meta_boxes' );

function do_my_meta_boxes( $post_type ) {
    remove_meta_box( 'my_taxonomydiv', $post_type, 'side' );
    add_meta_box( 'my_taxonomydiv', 'My Taxonomy', 'my_meta_box', $post_type, 'side' );
}

function my_meta_box( $post, $meta_box ) {

    $taxonomy = 'my_taxonomy';
    $tax      = get_taxonomy( $taxonomy );
    $selected = wp_get_object_terms( $post->ID, $taxonomy, array( 'fields' => 'ids' ) );

    ?>
    <div id="taxonomy-<?php echo $taxonomy; ?>" class="categorydiv">

        <input type="hidden" name="tax_input[<?php echo $taxonomy; ?>][]" value="0" />

        <ul id="<?php echo $taxonomy; ?>checklist" class="list:<?php echo $taxonomy; ?> categorychecklist form-no-clear">
            <?php
                wp_terms_checklist( $post->ID, array(
                    'taxonomy'      => $taxonomy,
                    'selected_cats' => $selected
                ) );
            ?>
        </ul>

    </div>
    <?php

}

?>