<?xml version="1.0" encoding="UTF-8"?>
<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="https://github.com/emdb-empiar/emdb-schemas/blob/master/v3/v3_0_1_7/emdb.xsd" emdb_id="EMD-10341" version="3.0.1.7">
    <admin>
        <current_status>
            <date>2020-01-22</date>
            <code>REL</code>
            <processing_site>PDBe</processing_site>
        </current_status>
        <sites>
            <deposition>PDBe</deposition>
            <last_processing>PDBe</last_processing>
        </sites>
        <key_dates>
            <deposition>2019-09-26</deposition>
            <header_release>2020-01-22</header_release>
            <map_release>2020-01-22</map_release>
            <update>2020-01-22</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>Medical Research Council (United Kingdom)</funding_body>
                <code>MR/P019374/1</code>
                <country>United Kingdom</country>
            </grant_reference>
        </grant_support>
        <title>Campylobacter jejuni fliN deletion bacterial flagella motor</title>
        <authors_list>
            <author>Henderson LD</author>
            <author>Beeby M</author>
        </authors_list>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Henderson LD</author>
                    <author order="2">Matthews-Palmer TRS</author>
                    <author order="3">Gulbronson CJ</author>
                    <author order="4">Ribardo DA</author>
                    <author order="5">Beeby M</author>
                    <author order="6">Hendrixson DR</author>
                    <title>Diversification of Campylobacter jejuni Flagellar C-Ring Composition Impacts Its Structure and Function in Motility, Flagellar Assembly, and Cellular Processes.</title>
                    <journal_abbreviation>Mbio</journal_abbreviation>
                    <country>US</country>
                    <volume>11</volume>
                    <year>2020</year>
                    <external_references type="PUBMED">31911488</external_references>
                    <external_references type="DOI">doi:10.1128/mBio.02286-19</external_references>
                    <external_references type="ISSN">2150-7511</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-10341</emdb_id>
                <relationship>
                    <other>associated EM volume</other>
                </relationship>
            </emdb_reference>
        </emdb_list>
    </crossreferences>
    <sample>
        <name>Bacterial flagellar motor (cellular-component from Campylobacter jejuni, located in [Cell wall])</name>
        <supramolecule_list>
            <organelle_or_cellular_component_supramolecule supramolecule_id="1">
                <name>Bacterial flagellar motor (cellular-component from Campylobacter jejuni, located in [Cell wall])</name>
                <parent>0</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>1</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <natural_source database="NCBI">
                    <organism ncbi="354242">Campylobacter jejuni subsp. jejuni 81-176</organism>
                    <cellular_location>Cell pole</cellular_location>
                </natural_source>
            </organelle_or_cellular_component_supramolecule>
        </supramolecule_list>
    </sample>
    <structure_determination_list>
        <structure_determination structure_determination_id="1">
            <method>subtomogramAveraging</method>
            <aggregation_state>cell</aggregation_state>
            <specimen_preparation_list>
                <subtomogram_averaging_preparation preparation_id="1">
                    <buffer>
                        <ph>7</ph>
                    </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>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE-PROPANE</cryogen_name>
                        <chamber_humidity units="percentage">95</chamber_humidity>
                        <chamber_temperature units="K">298</chamber_temperature>
                        <instrument>FEI VITROBOT MARK IV</instrument>
                        <details>Blot time 2, blot force 2, OD 20. </details>
                    </vitrification>
                    <details>In situ within Campylobacter jejuni</details>
                </subtomogram_averaging_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <subtomogram_averaging_microscopy microscopy_id="1">
                    <microscope>FEI TECNAI F20</microscope>
                    <illumination_mode>FLOOD BEAM</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>FIELD EMISSION GUN</electron_source>
                    <acceleration_voltage units="kV">200</acceleration_voltage>
                    <nominal_cs units="mm">2.0</nominal_cs>
                    <nominal_defocus_min units="µm">-2.5</nominal_defocus_min>
                    <nominal_defocus_max units="µm">-3.5</nominal_defocus_max>
                    <nominal_magnification>25000.0</nominal_magnification>
                    <specimen_holder_model>GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER</specimen_holder_model>
                    <cooling_holder_cryogen>NITROGEN</cooling_holder_cryogen>
                    <alignment_procedure>
                        <basic/>
                    </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>
                            <average_electron_dose_per_image units="e/Å^2">120.0</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>
                    <applied_symmetry>
                        <point_group>C17</point_group>
                    </applied_symmetry>
                    <algorithm>SIMULTANEOUS ITERATIVE (SIRT)</algorithm>
                    <resolution units="Å" res_type="BY AUTHOR">92.0</resolution>
                    <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>PEET</name>
                        </software>
                    </software_list>
                    <number_subtomograms_used>281</number_subtomograms_used>
                </final_reconstruction>
                <extraction>
                    <number_tomograms>300</number_tomograms>
                    <number_images_used>281</number_images_used>
                    <reference_model>Reference free</reference_model>
                    <method>Manually picked</method>
                    <software_list>
                        <software>
                            <name>IMOD</name>
                        </software>
                    </software_list>
                </extraction>
                <final_angle_assignment>
                    <type>NOT APPLICABLE</type>
                </final_angle_assignment>
            </subtomogram_averaging_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="13501">
        <file>emd_10341.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>150</col>
            <row>150</row>
            <sec>150</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>150</x>
            <y>150</y>
            <z>150</z>
        </spacing>
        <cell>
            <a units="Å">1242.15</a>
            <b units="Å">1242.15</b>
            <c units="Å">1242.15</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>-0.4414584</minimum>
            <maximum>0.41941792</maximum>
            <average>-0.06003719</average>
            <std>0.13994698</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">8.281</x>
            <y units="Å">8.281</y>
            <z units="Å">8.281</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.15</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-10341::::</label>
        <annotation_details>Main density map of Campylobacter jejuni %u0394FliN flagella motor structure.</annotation_details>
    </map>
</emd>
