<?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_2_0/emdb.xsd" emdb_id="EMD-11865" version="3.0.2.0">
    <admin>
        <current_status>
            <date>2020-12-02</date>
            <code>REL</code>
            <processing_site>PDBe</processing_site>
        </current_status>
        <sites>
            <deposition>PDBe</deposition>
            <last_processing>PDBe</last_processing>
        </sites>
        <key_dates>
            <deposition>2020-10-21</deposition>
            <header_release>2020-12-02</header_release>
            <map_release>2020-12-02</map_release>
            <update>2020-12-02</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>German Research Foundation (DFG)</funding_body>
                <code>SFB1129</code>
                <country>Germany</country>
            </grant_reference>
        </grant_support>
        <title>Tomogram of SARS-CoV-2 infected and cryo-FIB milled VeroE6 cells</title>
        <authors_list>
            <author>Klein S</author>
            <author>Cortese M</author>
            <author>Winter SL</author>
            <author>Wachsmuth-Melm M</author>
            <author>Neufeldt CJ</author>
            <author>Cerikan B</author>
            <author>Stanifer ML</author>
            <author>Boulant S</author>
            <author>Bartenschlager R</author>
            <author>Chlanda P</author>
        </authors_list>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Klein S</author>
                    <author order="2">Cortese M</author>
                    <author order="3">Winter SL</author>
                    <author order="4">Wachsmuth-Melm M</author>
                    <author order="5">Neufeldt CJ</author>
                    <author order="6">Cerikan B</author>
                    <author order="7">Stanifer ML</author>
                    <author order="8">Boulant S</author>
                    <author order="9">Bartenschlager R</author>
                    <author order="10">Chlanda P</author>
                    <title>SARS-CoV-2 structure and replication characterized by in situ cryo-electron tomography.</title>
                    <journal_abbreviation>Nat Commun</journal_abbreviation>
                    <country>UK</country>
                    <volume>11</volume>
                    <first_page>5885</first_page>
                    <last_page>5885</last_page>
                    <year>2020</year>
                    <external_references type="PUBMED">33208793</external_references>
                    <external_references type="DOI">doi:10.1038/s41467-020-19619-7</external_references>
                    <external_references type="ISSN">2041-1723</external_references>
                </journal_citation>
            </primary_citation>
            <secondary_citation>
                <journal_citation published="true">
                    <author order="11">Klein S</author>
                    <author order="12">Cortese M</author>
                    <author order="13">Winter SL</author>
                    <author order="14">Wachsmuth-Melm M</author>
                    <author order="15">Neufeldt CJ</author>
                    <author order="16">Cerikan B</author>
                    <author order="17">Stanifer ML</author>
                    <author order="18">Boulant S</author>
                    <author order="19">Bartenschlager R</author>
                    <author order="20">Chlanda P</author>
                    <title>SARS-CoV-2 structure and replication characterized by in situ cryo-electron tomography</title>
                    <journal_abbreviation>Biorxiv</journal_abbreviation>
                    <country>US</country>
                    <year>2020</year>
                    <external_references type="DOI">doi:10.1101/2020.06.23.167064</external_references>
                    <external_references type="CSD">0353</external_references>
                </journal_citation>
            </secondary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-11863</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-11865</emdb_id>
                <relationship>
                    <other>associated EM volume</other>
                </relationship>
            </emdb_reference>
        </emdb_list>
    </crossreferences>
    <sample>
        <name>VeroE6 cells infected with SARS-CoV-2</name>
        <supramolecule_list>
            <cell_supramolecule supramolecule_id="1">
                <name>VeroE6 cells infected with SARS-CoV-2</name>
                <parent>0</parent>
                <natural_source database="NCBI">
                    <organism ncbi="2697049">Severe acute respiratory syndrome coronavirus 2</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>
                    </buffer>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">70</chamber_humidity>
                        <chamber_temperature units="K">24</chamber_temperature>
                        <instrument>LEICA EM GP</instrument>
                        <details></details>
                    </vitrification>
                    <sectioning>
                        <focused_ion_beam>
                            <instrument>OTHER</instrument>
                            <ion>OTHER</ion>
                            <voltage units="kV">30</voltage>
                            <current units="nA">0.03</current>
                            <duration units="s">300</duration>
                            <temperature units="K">93</temperature>
                            <initial_thickness units="nm">4000</initial_thickness>
                            <final_thickness units="nm">150</final_thickness>
                            <details>The value given for _emd_sectioning_focused_ion_beam.instrument is Aquilos. This is not in a list of allowed values set(['DB235', 'OTHER']) so OTHER is written into the XML file.</details>
                        </focused_ion_beam>
                    </sectioning>
                </tomography_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <tomography_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>
                    <c2_aperture_diameter units="µm">70.0</c2_aperture_diameter>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>GATAN K3 BIOQUANTUM (6k x 4k)</film_or_detector_model>
                            <average_electron_dose_per_image units="e/Å^2">3.0</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>
                    <number_images_used>41</number_images_used>
                </final_reconstruction>
            </tomography_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="670434">
        <file>emd_11865.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS SIGNED BYTE</data_type>
        <dimensions>
            <col>1364</col>
            <row>1920</row>
            <sec>256</sec>
        </dimensions>
        <origin>
            <col>-278</col>
            <row>278</row>
            <sec>128</sec>
        </origin>
        <spacing>
            <x>1364</x>
            <y>1920</y>
            <z>256</z>
        </spacing>
        <cell>
            <a units="Å">10929.731</a>
            <b units="Å">15384.959</b>
            <c units="Å">2051.328</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>-0.5621532</average>
            <std>15.102742</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">8.013</x>
            <y units="Å">8.013</y>
            <z units="Å">8.013</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-11865::::</label>
    </map>
</emd>
