<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" emdb_id="EMD-4110" 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>2017-07-12</date>
            <code>REL</code>
            <processing_site>PDBe</processing_site>
        </current_status>
        <sites>
            <deposition>PDBe</deposition>
            <last_processing>PDBe</last_processing>
        </sites>
        <key_dates>
            <deposition>2016-10-14</deposition>
            <header_release>2016-11-09</header_release>
            <map_release>2016-11-09</map_release>
            <update>2017-07-12</update>
        </key_dates>
        <title>Respiratory complex I of Yarrowia lipolytica</title>
        <authors_list>
            <author>D'Imprima E</author>
            <author>Mills DJ</author>
            <author>Parey K</author>
            <author>Brandt U</author>
            <author>Kuehlbrandt W</author>
            <author>Zickermann V</author>
            <author>Vonck J</author>
        </authors_list>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">D'Imprima E</author>
                    <author order="2">Mills DJ</author>
                    <author order="3">Parey K</author>
                    <author order="4">Brandt U</author>
                    <author order="5">Kuhlbrandt W</author>
                    <author order="6">Zickermann V</author>
                    <author order="7">Vonck J</author>
                    <title>Cryo-EM structure of respiratory complex I reveals a link to mitochondrial sulfur metabolism.</title>
                    <journal_abbreviation>Biochim.Biophys.Acta</journal_abbreviation>
                    <country>NE</country>
                    <volume>1857</volume>
                    <first_page>1935</first_page>
                    <last_page>1942</last_page>
                    <year>2016</year>
                    <external_references type="PUBMED">27693469</external_references>
                    <external_references type="DOI">doi:10.1016/j.bbabio.2016.09.014</external_references>
                    <external_references type="ISSN">0006-3002</external_references>
                    <external_references type="CSD">0113</external_references>
                    <external_references type="ASTM">BBACAQ</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-4110</emdb_id>
                <relationship>
                    <other>associated EM volume</other>
                </relationship>
            </emdb_reference>
        </emdb_list>
    </crossreferences>
    <sample>
        <name>NADH:ubiquinone oxidoreductase</name>
        <supramolecule_list>
            <complex_supramolecule supramolecule_id="1">
                <name>NADH:ubiquinone oxidoreductase</name>
                <parent>0</parent>
                <natural_source database="NCBI">
                    <organism ncbi="4952">Yarrowia lipolytica</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">1</theoretical>
                </molecular_weight>
            </complex_supramolecule>
        </supramolecule_list>
    </sample>
    <structure_determination_list>
        <structure_determination structure_determination_id="1">
            <method>singleParticle</method>
            <aggregation_state>particle</aggregation_state>
            <specimen_preparation_list>
                <single_particle_preparation preparation_id="1">
                    <concentration units="mg/mL">3</concentration>
                    <buffer>
                        <ph>7.5</ph>
                        <component>
                            <concentration units="mM">30.0</concentration>
                            <name>Tris-HCl</name>
                        </component>
                        <component>
                            <concentration units="mM">100.0</concentration>
                            <formula>NaCl</formula>
                            <name>sodium chloride</name>
                        </component>
                    </buffer>
                    <grid>
                        <model>Quantifoil R2/2</model>
                        <material>COPPER</material>
                        <mesh>400</mesh>
                        <support_film film_type_id="1">
                            <film_material>CARBON</film_material>
                            <film_topology>HOLEY</film_topology>
                        </support_film>
                        <pretreatment>
                            <type>GLOW DISCHARGE</type>
                            <atmosphere>AIR</atmosphere>
                        </pretreatment>
                        <details>Before glow discharge the grids were pretreated in chloroform for 1-2 hrs</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">70</chamber_humidity>
                        <chamber_temperature units="K">283</chamber_temperature>
                        <instrument>FEI VITROBOT MARK IV</instrument>
                        <details>The samples were blotted for 8-10 seconds. </details>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_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>
                    <nominal_defocus_min units="&#181;m">1.3</nominal_defocus_min>
                    <calibrated_defocus_min units="&#181;m">1.3</calibrated_defocus_min>
                    <nominal_defocus_max units="&#181;m">4.5</nominal_defocus_max>
                    <calibrated_defocus_max units="&#181;m">4.5</calibrated_defocus_max>
                    <nominal_magnification>59000.</nominal_magnification>
                    <calibrated_magnification>79096.</calibrated_magnification>
                    <specimen_holder_model>OTHER</specimen_holder_model>
                    <cooling_holder_cryogen>NITROGEN</cooling_holder_cryogen>
                    <alignment_procedure>
                        <coma_free />
                    </alignment_procedure>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>FEI FALCON II (4k x 4k)</film_or_detector_model>
                            <detector_mode>INTEGRATING</detector_mode>
                            <digitization_details>
                                <dimensions>
                                    <width units="pixel">4096</width>
                                    <height units="pixel">4096</height>
                                </dimensions>
                                <sampling_interval units="&#181;m">14.0</sampling_interval>
                                <frames_per_image>2-24</frames_per_image>
                            </digitization_details>
                            <number_real_images>2250</number_real_images>
                            <average_exposure_time units="s">1.5</average_exposure_time>
                            <average_electron_dose_per_image units="e/&#8491;^2">84.0</average_electron_dose_per_image>
                            <details>Images were collected in movi-mode at 17 frames per second</details>
                        </image_recording>
                    </image_recording_list>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <image_recording_id>1</image_recording_id>
                <particle_selection>
                    <number_selected>50314</number_selected>
                    <details>particles were selected manually</details>
                </particle_selection>
                <ctf_correction>
                    <software_list>
                        <software>
                            <name>CTFFIND</name>
                            <version>3</version>
                        </software>
                    </software_list>
                </ctf_correction>
                <startup_model type_of_model="OTHER">
                    <details>A map was calculated from an undeposited x-ray structure of the same molecule</details>
                </startup_model>
                <final_reconstruction>
                    <number_classes_used>3</number_classes_used>
                    <applied_symmetry>
                        <point_group>C1</point_group>
                    </applied_symmetry>
                    <resolution res_type="BY AUTHOR" units="&#8491;">7.9</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>1.3</version>
                        </software>
                    </software_list>
                    <number_images_used>29125</number_images_used>
                </final_reconstruction>
                <initial_angle_assignment>
                    <type>OTHER</type>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>1.3</version>
                        </software>
                    </software_list>
                </initial_angle_assignment>
                <final_angle_assignment>
                    <type>PROJECTION MATCHING</type>
                    <projection_matching_processing />
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>1.3</version>
                        </software>
                    </software_list>
                </final_angle_assignment>
                <final_three_d_classification>
                    <number_classes>7</number_classes>
                </final_three_d_classification>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="44958">
        <file>emd_4110.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>224</col>
            <row>224</row>
            <sec>224</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>224</x>
            <y>224</y>
            <z>224</z>
        </spacing>
        <cell>
            <a units="&#8491;">396.47998</a>
            <b units="&#8491;">396.47998</b>
            <c units="&#8491;">396.47998</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>-0.036020786</minimum>
            <maximum>0.20733824</maximum>
            <average>0.0003321663</average>
            <std>0.014732352</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">1.7699999</x>
            <y units="&#8491;">1.7699999</y>
            <z units="&#8491;">1.7699999</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.085</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-4110::::</label>
        <annotation_details>respiratory complex I of Yarrowia lipolytica</annotation_details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <refinement_protocol>RIGID BODY FIT</refinement_protocol>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>