<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" emdb_id="EMD-1060" 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>2003-08-11</deposition>
         <header_release>2003-10-21</header_release>
         <map_release>2005-04-08</map_release>
         <update>2011-08-31</update>
      </key_dates>
      <title>Electron cryomicroscopy and bioinformatics suggest protein fold models for rice dwarf virus.</title>
      <authors_list>
         <author>Zhou ZH</author>
         <author>Baker ML</author>
         <author>Jiang W</author>
         <author>Dougherty M</author>
         <author>Jakana J</author>
         <author>Dong G</author>
         <author>Lu G</author>
         <author>Chiu W</author>
      </authors_list>
      <keywords>
         </keywords>
   </admin>
   <crossreferences>
      <citation_list>
         <primary_citation>
            <journal_citation published="true">
               <author order="1">Zhou ZH</author>
               <author order="2">Baker ML</author>
               <author order="3">Jiang W</author>
               <author order="4">Dougherty M</author>
               <author order="5">Jakana J</author>
               <author order="6">Dong G</author>
               <author order="7">Lu G</author>
               <author order="8">Chiu W</author>
               <title>Electron cryomicroscopy and bioinformatics suggest protein fold models for rice dwarf virus.</title>
               <journal>NAT.STRUCT.BIOL.</journal>
               <volume>8</volume>
               <first_page>868</first_page>
               <last_page>873</last_page>
               <year>2001</year>
               <external_references type="PUBMED">11573092</external_references>
               <external_references type="DOI">doi:10.1038/nsb1001-868</external_references>
            </journal_citation>
         </primary_citation>
      </citation_list>
   </crossreferences>
   <sample>
      <name>Rice Dwarf Virus</name>
      <supramolecule_list>
         <sample_supramolecule supramolecule_id="1000">
            <name>Rice Dwarf Virus</name>
            <details>Full capsid</details>
            <number_unique_components>1</number_unique_components>
            <molecular_weight>
               <theoretical units="MDa">50</theoretical>
            </molecular_weight>
         </sample_supramolecule>
         <virus_supramolecule supramolecule_id="1">
            <name synonym="rdv">Rice dwarf virus</name>
            <sci_species_name ncbi="10991">Rice dwarf virus</sci_species_name>
            <natural_host database="NCBI">
               <organism>
                  </organism>
               <synonym_organism>PLANTAE(HIGHER PLANTS)</synonym_organism>
            </natural_host>
            <host_system database="NCBI">
               </host_system>
            <virus_shell shell_id="1">
               <name>P3</name>
               <diameter units="&#8491;">590</diameter>
               <triangulation>1</triangulation>
            </virus_shell>
            <virus_shell shell_id="2">
               <name>P8</name>
               <diameter units="&#8491;">700</diameter>
               <triangulation>13</triangulation>
            </virus_shell>
            <virus_type>VIRION</virus_type>
            <virus_isolate>STRAIN</virus_isolate>
            <virus_enveloped>false</virus_enveloped>
            <virus_empty>false</virus_empty>
            <syn_species_name>rdv</syn_species_name>
         </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">
               <vitrification>
                  <cryogen_name>ETHANE</cryogen_name>
                  <chamber_humidity units="percentage">27</chamber_humidity>
                  <chamber_temperature units="K">111</chamber_temperature>
                  <instrument>HOMEMADE PLUNGER</instrument>
                  <details>Vitrification instrument: manual</details>
               </vitrification>
            </single_particle_preparation>
         </specimen_preparation_list>
         <microscopy_list>
            <single_particle_microscopy microscopy_id="1">
               <microscope>JEOL 4000</microscope>
               <illumination_mode>FLOOD BEAM</illumination_mode>
               <imaging_mode>BRIGHT FIELD</imaging_mode>
               <electron_source>LAB6</electron_source>
               <acceleration_voltage units="kV">400</acceleration_voltage>
               <nominal_cs units="mm">4.1</nominal_cs>
               <nominal_defocus_min units="&#181;m">0.3</nominal_defocus_min>
               <nominal_defocus_max units="&#181;m">2.2</nominal_defocus_max>
               <nominal_magnification>50000.0</nominal_magnification>
               <calibrated_magnification>49495.0</calibrated_magnification>
               <specimen_holder_model>GATAN LIQUID NITROGEN</specimen_holder_model>
               <temperature>
                  <temperature_average units="K">109</temperature_average>
               </temperature>
               <details>Microscope:JEOL 4000</details>
               <date>1999-01-01</date>
               <image_recording_list>
                  <image_recording>
                     <film_or_detector_model category="FILM">KODAK SO-163 FILM</film_or_detector_model>
                     <digitization_details>
                        <scanner>ZEISS SCAI</scanner>
                        <sampling_interval units="&#181;m">14</sampling_interval>
                     </digitization_details>
                     <number_real_images>162</number_real_images>
                     <average_electron_dose_per_image units="e/&#8491;^2">13</average_electron_dose_per_image>
                     <detector_distance>200</detector_distance>
                     <bits_per_pixel>12.</bits_per_pixel>
                  </image_recording>
               </image_recording_list>
               <specimen_holder>Gatan</specimen_holder>
            </single_particle_microscopy>
         </microscopy_list>
         <singleparticle_processing image_processing_id="1">
            <ctf_correction>
               <details>per micrograph</details>
            </ctf_correction>
            <final_reconstruction>
               <applied_symmetry>
                  <point_group>I</point_group>
               </applied_symmetry>
               <algorithm>OTHER</algorithm>
               <resolution res_type="BY AUTHOR" units="&#8491;">6.8</resolution>
               <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
               <software_list>
                  <software>
                     <name>MRC,IMRS</name>
                  </software>
               </software_list>
               <number_images_used>3261</number_images_used>
            </final_reconstruction>
         </singleparticle_processing>
      </structure_determination>
   </structure_determination_list>
   <map format="CCP4" size_kbytes="42571">
      <file>emd_1060.map.gz</file>
      <symmetry>
         <space_group>1</space_group>
      </symmetry>
      <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
      <dimensions>
         <col>279</col>
         <row>279</row>
         <sec>140</sec>
      </dimensions>
      <origin>
         <col>-139</col>
         <row>-139</row>
         <sec>-70</sec>
      </origin>
      <spacing>
         <x>279</x>
         <y>279</y>
         <z>140</z>
      </spacing>
      <cell>
         <a units="&#8491;">457.56</a>
         <b units="&#8491;">457.56</b>
         <c units="&#8491;">229.6</c>
         <alpha units="deg">90</alpha>
         <beta units="deg">90</beta>
         <gamma units="deg">90</gamma>
      </cell>
      <axis_order>
         <fast>X</fast>
         <medium>Y</medium>
         <slow>Z</slow>
      </axis_order>
      <statistics>
         <minimum>-8.18793</minimum>
         <maximum>9.502140000000001</maximum>
         <average>0.086981</average>
         <std>1.45153</std>
      </statistics>
      <pixel_spacing>
         <x units="&#8491;">1.64</x>
         <y units="&#8491;">1.64</y>
         <z units="&#8491;">1.64</z>
      </pixel_spacing>
      <contour_list>
         <contour primary="true">
            <level>0.38</level>
         </contour>
      </contour_list>
      <annotation_details>This is the 3f average map from Rice Dwarf Virus</annotation_details>
      <details>::::EMDATABANK.org::::EMD-1060::::</details>
   </map>
   <interpretation>
      <modelling_list>
         <modelling>
            <initial_model>
               <access_code>2BTV</access_code>
            </initial_model>
            <software_list>
               <software>
                  <name>Foldhunter</name>
               </software>
            </software_list>
            <details>FOLDHUNTER is decribed in Jiang et al , J.Mol.Biol., 308, 1033-1044 (2001). Beta sheet domain BTV VP7 blurred to 7 angstroms using the program PDB2MRC (Ludtke et at, J.Struct.Biol.,128, 82-97 (1999).</details>
            <overall_bvalue>100.0</overall_bvalue>
         </modelling>
      </modelling_list>
   </interpretation>
</emd>