<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" emdb_id="EMD-3559" 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>2017-08-30</date>
            <code>REL</code>
            <processing_site>PDBe</processing_site>
        </current_status>
        <sites>
            <deposition>PDBe</deposition>
            <last_processing>PDBe</last_processing>
        </sites>
        <key_dates>
            <deposition>2016-12-25</deposition>
            <header_release>2017-01-25</header_release>
            <map_release>2017-01-25</map_release>
            <update>2017-08-30</update>
        </key_dates>
        <title>mitochondrial ATP synthase dimer from Euglena gracilis</title>
        <authors_list>
            <author>Muehleip AW</author>
            <author>Davies KM</author>
            <author>Kuehlbrandt W</author>
        </authors_list>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Muhleip AW</author>
                    <author order="2">Dewar CE</author>
                    <author order="3">Schnaufer A</author>
                    <author order="4">Kuhlbrandt W</author>
                    <author order="5">Davies KM</author>
                    <title>In situ structure of trypanosomal ATP synthase dimer reveals a unique arrangement of catalytic subunits.</title>
                    <journal_abbreviation>Proc. Natl. Acad. Sci. U.S.A.</journal_abbreviation>
                    <country>US</country>
                    <volume>114</volume>
                    <first_page>992</first_page>
                    <last_page>997</last_page>
                    <year>2017</year>
                    <external_references type="PUBMED">28096380</external_references>
                    <external_references type="DOI">doi:10.1073/pnas.1612386114</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-3559</emdb_id>
                <relationship>
                    <other>associated EM volume</other>
                </relationship>
            </emdb_reference>
        </emdb_list>
    </crossreferences>
    <sample>
        <name>ATP synthase dimer from Euglena gracilis in isolated mitochondrial membranes</name>
        <supramolecule_list>
            <organelle_or_cellular_component_supramolecule supramolecule_id="1">
                <name>ATP synthase dimer from Euglena gracilis in isolated mitochondrial membranes</name>
                <parent>0</parent>
                <natural_source database="NCBI">
                    <organism ncbi="3039">Euglena gracilis</organism>
                    <organelle>mitochondrion</organelle>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">2</theoretical>
                </molecular_weight>
            </organelle_or_cellular_component_supramolecule>
        </supramolecule_list>
    </sample>
    <structure_determination_list>
        <structure_determination structure_determination_id="1">
            <method>subtomogramAveraging</method>
            <aggregation_state>threeDArray</aggregation_state>
            <specimen_preparation_list>
                <subtomogram_averaging_preparation preparation_id="1">
                    <buffer>
                        <ph>7.4</ph>
                        <component>
                            <concentration units="mM">20.0</concentration>
                            <formula>Tris</formula>
                            <name>tris(hydroxymethyl)aminomethane</name>
                        </component>
                        <component>
                            <concentration units="mM">250.0</concentration>
                            <formula>C12H22O11</formula>
                            <name>trehalose</name>
                        </component>
                    </buffer>
                    <grid>
                        <model>Quantifoil R2/2</model>
                        <material>COPPER</material>
                        <mesh>300</mesh>
                        <pretreatment>
                            <type>GLOW DISCHARGE</type>
                        </pretreatment>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">100</chamber_humidity>
                        <instrument>HOMEMADE PLUNGER</instrument>
                        <details>blot for 5s before plunging. </details>
                    </vitrification>
                </subtomogram_averaging_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <subtomogram_averaging_microscopy microscopy_id="1">
                    <microscope>FEI POLARA 300</microscope>
                    <illumination_mode>FLOOD BEAM</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>FIELD EMISSION GUN</electron_source>
                    <acceleration_voltage units="kV">300</acceleration_voltage>
                    <c2_aperture_diameter units="&#181;m">70.0</c2_aperture_diameter>
                    <nominal_cs units="mm">2.3</nominal_cs>
                    <nominal_defocus_min units="&#181;m">2.5</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">3.0</nominal_defocus_max>
                    <nominal_magnification>90000.</nominal_magnification>
                    <cooling_holder_cryogen>NITROGEN</cooling_holder_cryogen>
                    <temperature>
                        <temperature_min units="K">70.0</temperature_min>
                    </temperature>
                    <specialist_optics>
                        <energy_filter>
                            <name>GIF Quantum</name>
                            <lower_energy_threshold units="eV">0</lower_energy_threshold>
                            <upper_energy_threshold units="eV">20</upper_energy_threshold>
                        </energy_filter>
                    </specialist_optics>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>GATAN K2 SUMMIT (4k x 4k)</film_or_detector_model>
                            <detector_mode>COUNTING</detector_mode>
                            <digitization_details>
                                <dimensions>
                                    <width units="pixel">3838</width>
                                    <height units="pixel">3710</height>
                                </dimensions>
                                <frames_per_image>1-55</frames_per_image>
                            </digitization_details>
                            <average_electron_dose_per_image units="e/&#8491;^2">1.8</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                </subtomogram_averaging_microscopy>
            </microscopy_list>
            <subtomogram_averaging_processing image_processing_id="1">
                <image_recording_id>1</image_recording_id>
                <final_reconstruction>
                    <algorithm>BACK PROJECTION</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">27.5</resolution>
                    <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
                    <number_subtomograms_used>11</number_subtomograms_used>
                </final_reconstruction>
                <extraction>
                    <number_tomograms>11</number_tomograms>
                    <number_images_used>1294</number_images_used>
                    <reference_model>initial crude average</reference_model>
                    <method>volumes picked interactively</method>
                    <software_list>
                        <software>
                            <name>IMOD</name>
                        </software>
                    </software_list>
                </extraction>
                <ctf_correction>
                    <software_list>
                        <software>
                            <name>IMOD</name>
                        </software>
                    </software_list>
                </ctf_correction>
                <final_angle_assignment>
                    <type>OTHER</type>
                    <software_list>
                        <software>
                            <name>PEET</name>
                        </software>
                    </software_list>
                </final_angle_assignment>
            </subtomogram_averaging_processing>
        </structure_determination>
    </structure_determination_list>
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        <file>emd_3559.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>200</col>
            <row>200</row>
            <sec>200</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>200</x>
            <y>200</y>
            <z>200</z>
        </spacing>
        <cell>
            <a units="&#8491;">912.0</a>
            <b units="&#8491;">912.0</b>
            <c units="&#8491;">912.0</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>137.835630000000009</minimum>
            <maximum>164.425250000000005</maximum>
            <average>148.007200000000012</average>
            <std>0.85318077</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">4.56</x>
            <y units="&#8491;">4.56</y>
            <z units="&#8491;">4.56</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>153.</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-3559::::</label>
        <annotation_details>subtomogram average of mitochondrial ATP synthase dimer from Euglena gracilis</annotation_details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <refinement_protocol>RIGID BODY FIT</refinement_protocol>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>