<?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-30430" version="3.0.2.0">
    <admin>
        <current_status>
            <date>2020-11-11</date>
            <code>REL</code>
            <processing_site>PDBj</processing_site>
        </current_status>
        <sites>
            <deposition>PDBj</deposition>
            <last_processing>PDBj</last_processing>
        </sites>
        <key_dates>
            <deposition>2020-08-06</deposition>
            <header_release>2020-09-16</header_release>
            <map_release>2020-09-16</map_release>
            <update>2020-11-11</update>
        </key_dates>
        <title>the authentic SARS-CoV-2 virus</title>
        <authors_list>
            <author>Song Y</author>
            <author>Li S</author>
        </authors_list>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Yao H</author>
                    <author order="2">Song Y</author>
                    <author order="3">Chen Y</author>
                    <author order="4">Wu N</author>
                    <author order="5">Xu J</author>
                    <author order="6">Sun C</author>
                    <author order="7">Zhang J</author>
                    <author order="8">Weng T</author>
                    <author order="9">Zhang Z</author>
                    <author order="10">Wu Z</author>
                    <author order="11">Cheng L</author>
                    <author order="12">Shi D</author>
                    <author order="13">Lu X</author>
                    <author order="14">Lei J</author>
                    <author order="15">Crispin M</author>
                    <author order="16">Shi Y</author>
                    <author order="17">Li L</author>
                    <author order="18">Li S</author>
                    <title>Molecular Architecture of the SARS-CoV-2 Virus.</title>
                    <journal_abbreviation>Cell</journal_abbreviation>
                    <volume>183</volume>
                    <first_page>730</first_page>
                    <last_page>738.e13</last_page>
                    <year>2020</year>
                    <external_references type="PUBMED">32979942</external_references>
                    <external_references type="DOI">doi:10.1016/j.cell.2020.09.018</external_references>
                    <external_references type="ISSN">1097-4172</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-30430</emdb_id>
                <relationship>
                    <other>associated EM volume</other>
                </relationship>
            </emdb_reference>
        </emdb_list>
    </crossreferences>
    <sample>
        <name>Severe acute respiratory syndrome coronavirus 2</name>
        <supramolecule_list>
            <virus_supramolecule supramolecule_id="1">
                <name>Severe acute respiratory syndrome coronavirus 2</name>
                <parent>0</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>1</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <sci_species_name ncbi="2697049">Severe acute respiratory syndrome coronavirus 2</sci_species_name>
                <natural_host database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                </natural_host>
                <virus_shell shell_id="1">
                    <name>Envelope</name>
                    <diameter units="Å">120.0</diameter>
                </virus_shell>
                <virus_type>VIRION</virus_type>
                <virus_isolate>SPECIES</virus_isolate>
                <virus_enveloped>true</virus_enveloped>
                <virus_empty>false</virus_empty>
            </virus_supramolecule>
        </supramolecule_list>
    </sample>
    <structure_determination_list>
        <structure_determination structure_determination_id="1">
            <method>subtomogramAveraging</method>
            <aggregation_state>particle</aggregation_state>
            <specimen_preparation_list>
                <subtomogram_averaging_preparation preparation_id="1">
                    <buffer>
                        <ph>7.5</ph>
                    </buffer>
                    <grid>
                        <model>Quantifoil R2/2</model>
                        <material>COPPER</material>
                        <mesh>300</mesh>
                        <support_film film_type_id="1">
                            <film_material>CARBON</film_material>
                            <film_topology>HOLEY</film_topology>
                        </support_film>
                        <pretreatment>
                            <type>GLOW DISCHARGE</type>
                        </pretreatment>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">100</chamber_humidity>
                        <chamber_temperature units="K">20</chamber_temperature>
                        <instrument>GATAN CRYOPLUNGE 3</instrument>
                        <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>
                    <c2_aperture_diameter units="µm">70.0</c2_aperture_diameter>
                    <nominal_cs units="mm">2.7</nominal_cs>
                    <nominal_defocus_min units="µm">1.8</nominal_defocus_min>
                    <calibrated_defocus_min units="µm">1.8</calibrated_defocus_min>
                    <nominal_defocus_max units="µm">5.0</nominal_defocus_max>
                    <calibrated_defocus_max units="µm">4.0</calibrated_defocus_max>
                    <nominal_magnification>64000.0</nominal_magnification>
                    <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
                    <cooling_holder_cryogen>NITROGEN</cooling_holder_cryogen>
                    <specialist_optics>
                        <energy_filter>
                            <name>GIF Quantum LS</name>
                            <slit_width units="eV">20</slit_width>
                        </energy_filter>
                    </specialist_optics>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>GATAN K3 (6k x 4k)</film_or_detector_model>
                            <detector_mode>SUPER-RESOLUTION</detector_mode>
                            <digitization_details>
                                <dimensions>
                                    <width units="pixel">5760</width>
                                    <height units="pixel">4092</height>
                                </dimensions>
                                <frames_per_image>1-8</frames_per_image>
                            </digitization_details>
                            <average_exposure_time units="s">0.8</average_exposure_time>
                            <average_electron_dose_per_image units="e/Å^2">3.2</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>C1</point_group>
                    </applied_symmetry>
                    <resolution units="Å" res_type="BY AUTHOR">12.0</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>Dynamo</name>
                            <version>1.1.333</version>
                        </software>
                    </software_list>
                    <details>A combined virus model by projection of refined structures of its spikes and RNPs.</details>
                    <number_subtomograms_used>2294</number_subtomograms_used>
                </final_reconstruction>
                <extraction>
                    <number_tomograms>319</number_tomograms>
                    <number_images_used>2294</number_images_used>
                    <software_list>
                        <software>
                            <name>Dynamo</name>
                            <version>1.1.333</version>
                        </software>
                    </software_list>
                </extraction>
                <ctf_correction>
                    <software_list>
                        <software>
                            <name>Gctf</name>
                        </software>
                        <software>
                            <name>NOVACTF</name>
                        </software>
                    </software_list>
                </ctf_correction>
                <final_three_d_classification>
                    <software_list>
                        <software>
                            <name>Dynamo</name>
                            <version>1.1.333</version>
                        </software>
                    </software_list>
                </final_three_d_classification>
                <final_angle_assignment>
                    <type>OTHER</type>
                    <software_list>
                        <software>
                            <name>Dynamo</name>
                            <version>1.1.333</version>
                        </software>
                    </software_list>
                    <details>Subtomogram averaging</details>
                </final_angle_assignment>
            </subtomogram_averaging_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="536871">
        <file>emd_30430.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>512</col>
            <row>512</row>
            <sec>512</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>512</x>
            <y>512</y>
            <z>512</z>
        </spacing>
        <cell>
            <a units="Å">1392.64</a>
            <b units="Å">1392.64</b>
            <c units="Å">1392.64</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>-14.844941</minimum>
            <maximum>230.03519</maximum>
            <average>2.1398869</average>
            <std>13.098137</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">2.72</x>
            <y units="Å">2.72</y>
            <z units="Å">2.72</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>1.5</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-30430::::</label>
        <annotation_details>the authentic SARS-CoV-2 virus</annotation_details>
    </map>
</emd>
