<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" emdb_id="EMD-3351" version="3.0.1.1" xsi:schemaLocation="https://github.com/emdb-empiar/emdb-schemas/blob/master/v3/v3_0_1_1/emdb_relaxed.xsd">
   <admin>
      <current_status>
         <code>REL</code>
         <processing_site>PDBe</processing_site>
      </current_status>
      <sites>
         <deposition>PDBe</deposition>
         <last_processing>PDBe</last_processing>
      </sites>
      <key_dates>
         <deposition>2016-03-01</deposition>
         <header_release>2016-03-09</header_release>
         <map_release>2016-09-28</map_release>
         <update>2017-01-18</update>
      </key_dates>
      <title>Electron cryo-microscopy of an dsRNA-full Omono River virus (OmRV)</title>
      <authors_list>
         <author>Okamoto K</author>
         <author>Miyazaki N</author>
         <author>Larsson DSD</author>
         <author>Kobayashi D</author>
         <author>Svenda M</author>
         <author>Muehlig K</author>
         <author>Maia FRNC</author>
         <author>Gunn L-H</author>
         <author>Isawa H</author>
         <author>Kobayashi M</author>
         <author>Sawabe K</author>
         <author>Murata K</author>
         <author>Hajdu J</author>
      </authors_list>
      <keywords>Virus, totivirus, mosquito, totiviridae, double-stranded RNA, dsRNA, capsid, icosahedral, icosahedron, T=1</keywords>
   </admin>
   <crossreferences>
      <citation_list>
         <primary_citation>
            <journal_citation published="true">
               <author order="1">Okamoto K</author>
               <author order="2">Miyazaki N</author>
               <author order="3">Larsson DSD</author>
               <author order="4">Kobayashi D</author>
               <author order="5">Svenda M</author>
               <author order="6">Muehlig K</author>
               <author order="7">Maia FRNC</author>
               <author order="8">Gunn L-H</author>
               <author order="9">Isawa H</author>
               <author order="10">Kobayashi M</author>
               <author order="11">Sawabe K</author>
               <author order="12">Murata K</author>
               <author order="13">Hajdu J</author>
               <title>The infectious totivirus-like particle of insect-borne Omono River virus has raised ridges and lacks fibre complexes</title>
               <journal>Sci. Rep.</journal>
               <volume>6</volume>
               <first_page>33170</first_page>
               <year>2016</year>
               <external_references type="PUBMED">27616740</external_references>
               <external_references type="DOI">doi:10.1038/srep33170</external_references>
            </journal_citation>
         </primary_citation>
      </citation_list>
   </crossreferences>
   <sample>
      <name>dsRNA-full totivirus-like Omono River virus (OmRV)</name>
      <supramolecule_list>
         <sample_supramolecule supramolecule_id="1000">
            <name>dsRNA-full totivirus-like Omono River virus (OmRV)</name>
            <oligomeric_state>T=1 (T=2)</oligomeric_state>
            <number_unique_components>1</number_unique_components>
         </sample_supramolecule>
         <virus_supramolecule supramolecule_id="1">
            <name>Omono River virus</name>
            <details>dsRNA-filled particle</details>
            <sci_species_name ncbi="753758">Omono River virus</sci_species_name>
            <natural_host database="NCBI">
               <organism>Culex mosquito</organism>
               <synonym_organism>INVERTEBRATES</synonym_organism>
            </natural_host>
            <host_system database="NCBI">
               </host_system>
            <virus_shell shell_id="1">
               <name>capsid</name>
               <diameter units="&#8491;">61</diameter>
               <triangulation>1</triangulation>
            </virus_shell>
            <virus_type>VIRION</virus_type>
            <virus_isolate>SPECIES</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">1.43</concentration>
               <buffer>
                  <ph>7.5</ph>
                  <details>100 mM ammonium acetate</details>
               </buffer>
               <grid>
                  <details>Holey carbon grid</details>
               </grid>
               <vitrification>
                  <cryogen_name>ETHANE</cryogen_name>
                  <instrument>FEI VITROBOT MARK III</instrument>
               </vitrification>
            </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>
               <nominal_cs units="mm">4.2</nominal_cs>
               <nominal_defocus_min units="&#181;m">0.001</nominal_defocus_min>
               <nominal_defocus_max units="&#181;m">0.003</nominal_defocus_max>
               <nominal_magnification>50000.0</nominal_magnification>
               <specimen_holder_model>JEOL</specimen_holder_model>
               <specialist_optics>
                  <energy_filter>
                     <name>Omega</name>
                  </energy_filter>
               </specialist_optics>
               <date>2016-01-13</date>
               <image_recording_list>
                  <image_recording>
                     <film_or_detector_model category="CCD">TVIPS TEMCAM-F416 (4k x 4k)</film_or_detector_model>
                     <average_electron_dose_per_image units="e/&#8491;^2">20</average_electron_dose_per_image>
                  </image_recording>
               </image_recording_list>
               <specimen_holder>Liquid nitrogen cooled</specimen_holder>
            </single_particle_microscopy>
         </microscopy_list>
         <singleparticle_processing image_processing_id="1">
            <final_reconstruction>
               <applied_symmetry>
                  <point_group>I</point_group>
               </applied_symmetry>
               <resolution res_type="BY AUTHOR" units="&#8491;">8.9</resolution>
               <resolution_method>OTHER</resolution_method>
               <software_list>
                  <software>
                     <name>EMAN2, RELION</name>
                  </software>
               </software_list>
               <number_images_used>6224</number_images_used>
            </final_reconstruction>
         </singleparticle_processing>
      </structure_determination>
   </structure_determination_list>
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      <file>emd_3351.map.gz</file>
      <symmetry>
         <space_group>1</space_group>
      </symmetry>
      <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
      <dimensions>
         <col>280</col>
         <row>280</row>
         <sec>280</sec>
      </dimensions>
      <origin>
         <col>0</col>
         <row>0</row>
         <sec>0</sec>
      </origin>
      <spacing>
         <x>280</x>
         <y>280</y>
         <z>280</z>
      </spacing>
      <cell>
         <a units="&#8491;">526.4</a>
         <b units="&#8491;">526.4</b>
         <c units="&#8491;">526.4</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>-0.19810656</minimum>
         <maximum>0.91002715</maximum>
         <average>0.01812066</average>
         <std>0.04449147</std>
      </statistics>
      <pixel_spacing>
         <x units="&#8491;">1.8800001</x>
         <y units="&#8491;">1.8800001</y>
         <z units="&#8491;">1.8800001</z>
      </pixel_spacing>
      <contour_list>
         <contour primary="true">
            <level>0.0938</level>
            <source>AUTHOR</source>
         </contour>
      </contour_list>
      <annotation_details>Reconstruction of dsRNA-full OmRV</annotation_details>
      <details>::::EMDATABANK.org::::EMD-3351::::</details>
   </map>
</emd>