<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" emdb_id="EMD-0130" version="3.0.0.1" xsi:schemaLocation="https://github.com/emdb-empiar/emdb-schemas/blob/master/v3/v3_0_0_1/emdb.xsd">
    <admin>
        <current_status>
            <date>2018-11-07</date>
            <code>REL</code>
            <processing_site>PDBe</processing_site>
        </current_status>
        <sites>
            <deposition>PDBe</deposition>
            <last_processing>PDBe</last_processing>
        </sites>
        <key_dates>
            <deposition>2018-07-13</deposition>
            <header_release>2018-08-22</header_release>
            <map_release>2018-11-07</map_release>
            <update>2018-11-07</update>
        </key_dates>
        <title>Structure of the Macrobrachium rosenbergii Nodavirus</title>
        <authors_list>
            <author>Ho KH</author>
            <author>Gabrielsen M</author>
        </authors_list>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Ho KL</author>
                    <author order="2">Gabrielsen M</author>
                    <author order="3">Beh PL</author>
                    <author order="4">Kueh CL</author>
                    <author order="5">Thong QX</author>
                    <author order="6">Streetley J</author>
                    <author order="7">Tan WS</author>
                    <author order="8">Bhella D</author>
                    <title>Structure of the Macrobrachium rosenbergii nodavirus: A new genus within the Nodaviridae?</title>
                    <journal_abbreviation>PLoS Biol.</journal_abbreviation>
                    <country>US</country>
                    <volume>16</volume>
                    <first_page>e3000038</first_page>
                    <last_page>e3000038</last_page>
                    <year>2018</year>
                    <external_references type="PUBMED">30346944</external_references>
                    <external_references type="DOI">doi:10.1371/journal.pbio.3000038</external_references>
                    <external_references type="ISSN">1545-7885</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-0129</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
                <details>EMD 0129 contains a 3.3 angstrom structure of a VLP produced by recombinant expression of MrNV capsid protein</details>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-0130</emdb_id>
                <relationship>
                    <other>associated EM volume</other>
                </relationship>
            </emdb_reference>
        </emdb_list>
    </crossreferences>
    <sample>
        <name>Macrobrachium rosen</name>
        <supramolecule_list>
            <virus_supramolecule supramolecule_id="1">
                <name>Macrobrachium rosen</name>
                <parent>0</parent>
                <details>Virions were purified from Macrobrachium rosenbergii infected post-larvae</details>
                <sci_species_name ncbi="32644">Macrobrachium rosen</sci_species_name>
                <natural_host database="NCBI">
                    <organism ncbi="79674">Macrobrachium rosenbergii</organism>
                </natural_host>
                <virus_shell shell_id="1">
                    <name>Capsid</name>
                    <diameter units="&#8491;">400.0</diameter>
                    <triangulation>3</triangulation>
                </virus_shell>
                <virus_type>VIRION</virus_type>
                <virus_isolate>OTHER</virus_isolate>
                <virus_enveloped>false</virus_enveloped>
                <virus_empty>false</virus_empty>
            </virus_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">0.2</concentration>
                    <buffer>
                        <ph>7.4</ph>
                        <details>25mM HEPES, 150 mM NaCl; pH 7.4</details>
                    </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>CONTINUOUS</film_topology>
                        </support_film>
                        <pretreatment>
                            <type>GLOW DISCHARGE</type>
                            <atmosphere>AIR</atmosphere>
                        </pretreatment>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">100</chamber_humidity>
                        <chamber_temperature units="K">277</chamber_temperature>
                        <instrument>FEI VITROBOT MARK IV</instrument>
                        <details>Virions were loaded onto Quantifoil R2/2 grids which had a continuous carbon film added. Virions were adsorbed to the carbon for 1 minute prior to blotting (4s).. </details>
                    </vitrification>
                    <details>Purified virions</details>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>JEOL 2200FS</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>
                    <specimen_holder_model>GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER</specimen_holder_model>
                    <specialist_optics>
                        <energy_filter>
                            <name>In-column Omega Filter</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>DIRECT ELECTRON DE-20 (5k x 3k)</film_or_detector_model>
                            <detector_mode>INTEGRATING</detector_mode>
                            <digitization_details>
                                <frames_per_image>2-40</frames_per_image>
                            </digitization_details>
                            <number_real_images>263</number_real_images>
                            <average_exposure_time units="s">2.0</average_exposure_time>
                            <average_electron_dose_per_image units="e/&#8491;^2">60.0</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <image_recording_id>1</image_recording_id>
                <details>Movies were processed to correct for movement and electron dose using Motioncor2</details>
                <particle_selection>
                    <number_selected>7236</number_selected>
                    <details>Autopicking in Relion</details>
                </particle_selection>
                <ctf_correction>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>2.1</version>
                        </software>
                    </software_list>
                    <details>Defocus estimation by GCTF</details>
                </ctf_correction>
                <startup_model type_of_model="OTHER">
                    <details>Gaussian Sphere</details>
                </startup_model>
                <final_reconstruction>
                    <applied_symmetry>
                        <point_group>I</point_group>
                    </applied_symmetry>
                    <resolution res_type="BY AUTHOR" units="&#8491;">6.6</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>2.1</version>
                        </software>
                    </software_list>
                    <number_images_used>3931</number_images_used>
                </final_reconstruction>
                <initial_angle_assignment>
                    <type>PROJECTION MATCHING</type>
                    <projection_matching_processing />
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>2.1</version>
                        </software>
                    </software_list>
                </initial_angle_assignment>
                <final_angle_assignment>
                    <type>PROJECTION MATCHING</type>
                    <projection_matching_processing />
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>2.1</version>
                        </software>
                    </software_list>
                </final_angle_assignment>
                <final_three_d_classification>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>2.1</version>
                        </software>
                    </software_list>
                </final_three_d_classification>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="536871">
        <file>emd_0130.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="&#8491;">568.32</a>
            <b units="&#8491;">568.32</b>
            <c units="&#8491;">568.32</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>-0.016487258</minimum>
            <maximum>0.09236631</maximum>
            <average>0.003213234</average>
            <std>0.010186772</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">1.11</x>
            <y units="&#8491;">1.11</y>
            <z units="&#8491;">1.11</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.035</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-0130::::</label>
        <annotation_details>CryoEM reconstruction of Macrobrachium rosenbergii nodavirus virion</annotation_details>
    </map>
</emd>