<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" emdb_id="EMD-2782" 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>2014-09-07</deposition>
         <header_release>2014-10-08</header_release>
         <map_release>2015-11-25</map_release>
         <update>2016-03-02</update>
      </key_dates>
      <title>Cryo-electron microscopy of Rice dwarf virus virion</title>
      <authors_list>
         <author>Miyazaki N</author>
         <author>Higashiura A</author>
         <author>Higashiura T</author>
         <author>Akita F</author>
         <author>Hibino H</author>
         <author>Omura T</author>
         <author>Nakagawa A</author>
         <author>Iwasaki K</author>
      </authors_list>
      <keywords>Rice dwarf virus, Phytoreovirus, Reoviridae family, Virus particle</keywords>
   </admin>
   <crossreferences>
      <citation_list>
         <primary_citation>
            <journal_citation published="true">
               <author order="1">Miyazaki N</author>
               <author order="2">Higashiura A</author>
               <author order="3">Higashiura T</author>
               <author order="4">Akita F</author>
               <author order="5">Hibino H</author>
               <author order="6">Omura T</author>
               <author order="7">Nakagawa A</author>
               <author order="8">Iwasaki K</author>
               <title>Electron microscopic imaging revealed the flexible filamentous structure of the cell attachment protein P2 of Rice dwarf virus located around the icosahedral 5-fold axes.</title>
               <journal>J.BIOCHEM.</journal>
               <volume>159</volume>
               <first_page>181</first_page>
               <last_page>190</last_page>
               <year>2016</year>
               <external_references type="PUBMED">26374901</external_references>
               <external_references type="DOI">doi:10.1093/jb/mvv092</external_references>
            </journal_citation>
         </primary_citation>
      </citation_list>
   </crossreferences>
   <sample>
      <name>Rice dwarf virus virion</name>
      <supramolecule_list>
         <sample_supramolecule supramolecule_id="1000">
            <name>Rice dwarf virus virion</name>
            <oligomeric_state>Icosahedral particle</oligomeric_state>
            <number_unique_components>1</number_unique_components>
            <molecular_weight>
               <experimental units="MDa">75</experimental>
               <theoretical units="MDa">75</theoretical>
            </molecular_weight>
         </sample_supramolecule>
         <virus_supramolecule supramolecule_id="1">
            <name>Rice dwarf virus</name>
            <sci_species_name ncbi="10991">Rice dwarf virus</sci_species_name>
            <natural_host database="NCBI">
               <organism ncbi="4530">Oryza sativa</organism>
               <synonym_organism>PLANTAE(HIGHER PLANTS)</synonym_organism>
            </natural_host>
            <host_system database="NCBI">
               </host_system>
            <molecular_weight>
               <experimental units="MDa">75</experimental>
               <theoretical units="MDa">75</theoretical>
            </molecular_weight>
            <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">
               <buffer>
                  <ph>6.2</ph>
                  <details>100mM Histidine, 10mM MgCl2</details>
               </buffer>
               <vitrification>
                  <cryogen_name>ETHANE</cryogen_name>
                  <chamber_humidity units="percentage">100</chamber_humidity>
                  <chamber_temperature units="K">120</chamber_temperature>
                  <instrument>FEI VITROBOT MARK III</instrument>
               </vitrification>
            </single_particle_preparation>
         </specimen_preparation_list>
         <microscopy_list>
            <single_particle_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">200</acceleration_voltage>
               <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
               <date>2011-03-23</date>
               <image_recording_list>
                  <image_recording>
                     <film_or_detector_model category="CCD">GATAN ULTRASCAN 4000 (4k x 4k)</film_or_detector_model>
                  </image_recording>
               </image_recording_list>
            </single_particle_microscopy>
         </microscopy_list>
         <singleparticle_processing image_processing_id="1">
            <ctf_correction>
               <details>Each particle</details>
            </ctf_correction>
            <final_reconstruction>
               <applied_symmetry>
                  <point_group>I</point_group>
               </applied_symmetry>
               <resolution res_type="BY AUTHOR" units="&#8491;">13.0</resolution>
               <resolution_method>OTHER</resolution_method>
               <software_list>
                  <software>
                     <name>EMAN2</name>
                  </software>
               </software_list>
               <number_images_used>1034</number_images_used>
            </final_reconstruction>
         </singleparticle_processing>
      </structure_determination>
   </structure_determination_list>
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      <file>emd_2782.map.gz</file>
      <symmetry>
         <space_group>1</space_group>
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      <dimensions>
         <col>400</col>
         <row>400</row>
         <sec>400</sec>
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      <origin>
         <col>-200</col>
         <row>-200</row>
         <sec>-200</sec>
      </origin>
      <spacing>
         <x>400</x>
         <y>400</y>
         <z>400</z>
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      <cell>
         <a units="&#8491;">1172.0</a>
         <b units="&#8491;">1172.0</b>
         <c units="&#8491;">1172.0</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>
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         <minimum>-11.863731380000001</minimum>
         <maximum>8.87250996</maximum>
         <average>0.00764933</average>
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         <y units="&#8491;">2.93</y>
         <z units="&#8491;">2.93</z>
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      <contour_list>
         <contour primary="true">
            <level>0.3</level>
            <source>AUTHOR</source>
         </contour>
      </contour_list>
      <annotation_details>3D reconstruction of Rice dwarf virus virion</annotation_details>
      <details>::::EMDATABANK.org::::EMD-2782::::</details>
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