<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" emdb_id="EMD-3606" version="3.0.0.0" xsi:schemaLocation="https://github.com/emdb-empiar/emdb-schemas/blob/master/v3/v3_0_0_0/emdb.xsd">
    <admin>
        <current_status>
            <date>2017-08-02</date>
            <code>REL</code>
            <processing_site>PDBe</processing_site>
        </current_status>
        <sites>
            <deposition>PDBe</deposition>
            <last_processing>PDBe</last_processing>
        </sites>
        <key_dates>
            <deposition>2017-02-28</deposition>
            <header_release>2017-03-22</header_release>
            <map_release>2017-03-22</map_release>
            <update>2017-08-02</update>
        </key_dates>
        <title>Malaria-infected red blood cell section showing a segmented schizont</title>
        <authors_list>
            <author>Hale VL</author>
            <author>Saibil HR</author>
        </authors_list>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Hale VL</author>
                    <author order="2">Watermeyer JM</author>
                    <author order="3">Hackett F</author>
                    <author order="4">Vizcay-Barrena G</author>
                    <author order="5">van Ooij C</author>
                    <author order="6">Thomas JA</author>
                    <author order="7">Spink MC</author>
                    <author order="8">Harkiolaki M</author>
                    <author order="9">Duke E</author>
                    <author order="10">Fleck RA</author>
                    <author order="11">Blackman MJ</author>
                    <author order="12">Saibil HR</author>
                    <title>Parasitophorous vacuole poration precedes its rupture and rapid host erythrocyte cytoskeleton collapse in Plasmodium falciparum egress.</title>
                    <journal_abbreviation>Proc. Natl. Acad. Sci. U.S.A.</journal_abbreviation>
                    <country>US</country>
                    <volume>114</volume>
                    <first_page>3439</first_page>
                    <last_page>3444</last_page>
                    <year>2017</year>
                    <external_references type="PUBMED">28292906</external_references>
                    <external_references type="DOI">doi:10.1073/pnas.1619441114</external_references>
                    <external_references type="ISSN">1091-6490</external_references>
                    <external_references type="CSD">0040</external_references>
                    <external_references type="ASTM">PNASA6</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-3606</emdb_id>
                <relationship>
                    <other>associated EM volume</other>
                </relationship>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-3586</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
                <details>3586 is a resin section tomogram of the same cells at an earlier stage in development.</details>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-3587</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
                <details>3587 is a resin section tomogram of the same cells treated with E64, an inhibitor that traps the parasites in an intermediate stage of egress.</details>
            </emdb_reference>
        </emdb_list>
    </crossreferences>
    <sample>
        <name>Plasmodium falciparum infected human erythrocyte treated with the egress inhibitor Compound 1</name>
        <supramolecule_list>
            <cell_supramolecule supramolecule_id="1">
                <name>Plasmodium falciparum infected human erythrocyte treated with the egress inhibitor Compound 1</name>
                <parent>0</parent>
                <details>High pressure frozen and freeze-substituted cell section</details>
                <natural_source database="NCBI">
                    <organism ncbi="36329">Plasmodium falciparum 3D7</organism>
                </natural_source>
            </cell_supramolecule>
        </supramolecule_list>
    </sample>
    <structure_determination_list>
        <structure_determination structure_determination_id="1">
            <method>tomography</method>
            <aggregation_state>cell</aggregation_state>
            <specimen_preparation_list>
                <tomography_preparation preparation_id="1">
                    <buffer>
                        <ph>7.</ph>
                        <details>RPMI medium</details>
                    </buffer>
                    <staining>
                        <type>NEGATIVE</type>
                        <material>Uranyl Acetate</material>
                    </staining>
                    <sugar_embedding>
                        <material>HM20</material>
                        <details>Freeze substitution</details>
                    </sugar_embedding>
                    <grid>
                        <material>COPPER</material>
                        <support_film film_type_id="1">
                            <film_material>CARBON</film_material>
                            <film_topology>CONTINUOUS</film_topology>
                        </support_film>
                        <pretreatment>
                            <type>GLOW DISCHARGE</type>
                        </pretreatment>
                    </grid>
                    <fiducial_markers_list>
                        <fiducial_marker>
                            <manufacturer>Electron Microscopy Sciences</manufacturer>
                            <diameter units="nanometer">10</diameter>
                        </fiducial_marker>
                    </fiducial_markers_list>
                    <high_pressure_freezing>
                        <instrument>OTHER</instrument>
                        <details>The value given for _emd_high_pressure_freezing.instrument is Baltech HPM010. This is not in a list of allowed values set(['LEICA EM PACT2', 'LEICA EM PACT', 'EMS-002 RAPID IMMERSION FREEZER', 'OTHER', 'LEICA EM HPM100', 'BAL-TEC HPM 010']) so OTHER is written into the XML file.</details>
                    </high_pressure_freezing>
                    <sectioning>
                        <ultramicrotomy>
                            <instrument>Leica EM UC7</instrument>
                            <temperature units="K">293</temperature>
                            <final_thickness>100</final_thickness>
                        </ultramicrotomy>
                    </sectioning>
                </tomography_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <tomography_microscopy microscopy_id="1">
                    <microscope>FEI TECNAI 12</microscope>
                    <illumination_mode>FLOOD BEAM</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>TUNGSTEN HAIRPIN</electron_source>
                    <acceleration_voltage units="kV">120</acceleration_voltage>
                    <specimen_holder_model>OTHER</specimen_holder_model>
                    <alignment_procedure>
                        <basic />
                    </alignment_procedure>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>GATAN ULTRASCAN 1000 (2k x 2k)</film_or_detector_model>
                            <average_electron_dose_per_image units="e/&#8491;^2">100.0</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                </tomography_microscopy>
            </microscopy_list>
            <tomography_processing image_processing_id="1">
                <image_recording_id>1</image_recording_id>
                <final_reconstruction>
                    <algorithm>BACK PROJECTION</algorithm>
                    <software_list>
                        <software>
                            <name>IMOD</name>
                        </software>
                    </software_list>
                    <number_images_used>127</number_images_used>
                </final_reconstruction>
            </tomography_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="74804">
        <file>emd_3606.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS SIGNED BYTE</data_type>
        <dimensions>
            <col>957</col>
            <row>965</row>
            <sec>81</sec>
        </dimensions>
        <origin>
            <col>-53</col>
            <row>-45</row>
            <sec>40</sec>
        </origin>
        <spacing>
            <x>957</x>
            <y>965</y>
            <z>81</z>
        </spacing>
        <cell>
            <a units="&#8491;">15558.867</a>
            <b units="&#8491;">15688.929</b>
            <c units="&#8491;">1316.8947</c>
            <alpha units="deg">90.0</alpha>
            <beta units="deg">90.0</beta>
            <gamma units="deg">90.0</gamma>
        </cell>
        <axis_order>
            <fast>X</fast>
            <medium>Y</medium>
            <slow>Z</slow>
        </axis_order>
        <statistics>
            <minimum>-128.</minimum>
            <maximum>127.</maximum>
            <average>93.034180000000006</average>
            <std>6.297862</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">16.25796</x>
            <y units="&#8491;">16.257957</y>
            <z units="&#8491;">16.25796</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-3606::::</label>
        <annotation_details>Resin section tomogram of a malaria infected red blood cell showing a fully segmented schizont.</annotation_details>
    </map>
</emd>