<?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_9/emdb.xsd" emdb_id="EMD-4561" version="3.0.1.9">
    <admin>
        <current_status>
            <date>2020-07-29</date>
            <code>REL</code>
            <processing_site>PDBe</processing_site>
        </current_status>
        <sites>
            <deposition>PDBe</deposition>
            <last_processing>PDBe</last_processing>
        </sites>
        <key_dates>
            <deposition>2019-01-21</deposition>
            <header_release>2019-03-27</header_release>
            <map_release>2019-03-27</map_release>
            <update>2020-07-29</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>European Research Council</funding_body>
                <country>Switzerland</country>
            </grant_reference>
        </grant_support>
        <title>STA of TssJLM</title>
        <authors_list>
            <author>Kooger R</author>
        </authors_list>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Rapisarda C</author>
                    <author order="2">Cherrak Y</author>
                    <author order="3">Kooger R</author>
                    <author order="4">Schmidt V</author>
                    <author order="5">Pellarin R</author>
                    <author order="6">Logger L</author>
                    <author order="7">Cascales E</author>
                    <author order="8">Pilhofer M</author>
                    <author order="9">Durand E</author>
                    <author order="10">Fronzes R</author>
                    <title>In situand high-resolution cryo-EM structure of a bacterial type VI secretion system membrane complex.</title>
                    <journal_abbreviation>Embo J.</journal_abbreviation>
                    <country>UK</country>
                    <volume>38</volume>
                    <year>2019</year>
                    <external_references type="PUBMED">30877094</external_references>
                    <external_references type="DOI">doi:10.15252/embj.2018100886</external_references>
                    <external_references type="ISSN">1460-2075</external_references>
                    <external_references type="CSD">0897</external_references>
                    <external_references type="ASTM">EMJODG</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-0264</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-4561</emdb_id>
                <relationship>
                    <other>associated EM volume</other>
                </relationship>
            </emdb_reference>
        </emdb_list>
    </crossreferences>
    <sample>
        <name>Membrane complex of the type 6 secretion system</name>
        <supramolecule_list>
            <complex_supramolecule supramolecule_id="1">
                <name>Membrane complex of the type 6 secretion system</name>
                <parent>0</parent>
                <natural_source database="NCBI">
                    <organism ncbi="216592">Escherichia coli 042</organism>
                </natural_source>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="469008">Escherichia coli BL21(DE3)</recombinant_organism>
                </recombinant_expression>
                <molecular_weight>
                    <experimental units="MDa">1.7</experimental>
                </molecular_weight>
            </complex_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>
                    <vitrification>
                        <cryogen_name>ETHANE-PROPANE</cryogen_name>
                        <details></details>
                    </vitrification>
                </subtomogram_averaging_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <subtomogram_averaging_microscopy microscopy_id="1">
                    <microscope>FEI TITAN KRIOS</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>
                    <specialist_optics>
                        <phase_plate>VOLTA PHASE PLATE</phase_plate>
                        <energy_filter>
                            <name>GIF Quantum LS</name>
                            <slit_width units="eV">30</slit_width>
                        </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>
                            <average_exposure_time units="s">3.0</average_exposure_time>
                            <average_electron_dose_per_image units="e/Å^2">1.3</average_electron_dose_per_image>
                            <details>STA from various tomograms taken with slightly different electron dose and frame</details>
                        </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>C5</point_group>
                    </applied_symmetry>
                    <algorithm>BACK PROJECTION</algorithm>
                    <resolution units="Å" res_type="BY AUTHOR">25.0</resolution>
                    <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>PEET</name>
                        </software>
                    </software_list>
                    <number_subtomograms_used>15000</number_subtomograms_used>
                </final_reconstruction>
                <extraction>
                    <number_tomograms>14</number_tomograms>
                    <number_images_used>25276</number_images_used>
                    <reference_model>one single particle</reference_model>
                </extraction>
                <final_angle_assignment>
                    <type>OTHER</type>
                </final_angle_assignment>
            </subtomogram_averaging_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="513">
        <file>emd_4561.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>40</col>
            <row>80</row>
            <sec>40</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>40</x>
            <y>80</y>
            <z>40</z>
        </spacing>
        <cell>
            <a units="Å">275.91998</a>
            <b units="Å">551.83997</b>
            <c units="Å">275.91998</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>93.403</minimum>
            <maximum>140.06</maximum>
            <average>110.36105</average>
            <std>3.5752475</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">6.898</x>
            <y units="Å">6.898</y>
            <z units="Å">6.898</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>113</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-4561::::</label>
        <annotation_details>TssJLM average as obtained by STA</annotation_details>
    </map>
</emd>
