<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" emdb_id="EMD-1580" 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>2008-11-04</deposition>
         <header_release>2008-11-05</header_release>
         <map_release>2009-04-01</map_release>
         <update>2011-09-09</update>
      </key_dates>
      <title>CryoEM and 3D image reconstruction of Chilo Iridescent virus at 13 angstrom resolution</title>
      <authors_list>
         <author>Yan X</author>
         <author>Yu Z</author>
         <author>Zhang P</author>
         <author>Battisti AJ</author>
         <author>Holdaway HA</author>
         <author>Chipman PR</author>
         <author>Bajaj C</author>
         <author>Bergoin M</author>
         <author>Rossmann MG</author>
         <author>Baker TS</author>
      </authors_list>
      <keywords>large DNA virus, cryo-electron microscopy, 3D image reconstruction, enveloped virus, minor capsid proteins</keywords>
   </admin>
   <crossreferences>
      <citation_list>
         <primary_citation>
            <journal_citation published="true">
               <author order="1">Yan X</author>
               <author order="2">Yu Z</author>
               <author order="3">Zhang P</author>
               <author order="4">Battisti AJ</author>
               <author order="5">Holdaway HA</author>
               <author order="6">Chipman PR</author>
               <author order="7">Bajaj C</author>
               <author order="8">Bergoin M</author>
               <author order="9">Rossmann MG</author>
               <author order="10">Baker TS</author>
               <title>The capsid proteins of a large, icosahedral dsDNA virus.</title>
               <journal>J.MOL.BIOL.</journal>
               <volume>385</volume>
               <first_page>1287</first_page>
               <last_page>1299</last_page>
               <year>2009</year>
               <external_references type="PUBMED">19027752</external_references>
               <external_references type="DOI">doi:10.1016/j.jmb.2008.11.002</external_references>
            </journal_citation>
         </primary_citation>
      </citation_list>
   </crossreferences>
   <sample>
      <name>CIV</name>
      <supramolecule_list>
         <sample_supramolecule supramolecule_id="1000">
            <name>CIV</name>
            <details>CIV virions</details>
            <number_unique_components>1</number_unique_components>
         </sample_supramolecule>
         <virus_supramolecule supramolecule_id="1">
            <name synonym="chilo iridescent virus">Invertebrate iridescent virus 6</name>
            <sci_species_name ncbi="176652">Invertebrate iridescent virus 6</sci_species_name>
            <natural_host database="NCBI">
               <organism ncbi="7088">Lepidoptera</organism>
               <synonym_organism>INVERTEBRATES</synonym_organism>
            </natural_host>
            <host_system database="NCBI">
               </host_system>
            <virus_shell shell_id="1">
               <diameter units="&#8491;">1850</diameter>
            </virus_shell>
            <virus_type>VIRION</virus_type>
            <virus_isolate>SPECIES</virus_isolate>
            <virus_enveloped>true</virus_enveloped>
            <virus_empty>false</virus_empty>
            <syn_species_name>chilo iridescent virus</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">
               <grid>
                  <details>holey carbon film</details>
               </grid>
               <vitrification>
                  <cryogen_name>NITROGEN</cryogen_name>
                  <instrument>HOMEMADE PLUNGER</instrument>
                  <details>Vitrification instrument: manual plunger</details>
               </vitrification>
            </single_particle_preparation>
         </specimen_preparation_list>
         <microscopy_list>
            <single_particle_microscopy microscopy_id="1">
               <microscope>FEI/PHILIPS CM300FEG/T</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>
               <nominal_cs units="mm">2.0</nominal_cs>
               <nominal_defocus_min units="&#181;m">0.8</nominal_defocus_min>
               <nominal_defocus_max units="&#181;m">3.0</nominal_defocus_max>
               <nominal_magnification>33000.0</nominal_magnification>
               <calibrated_magnification>33000.0</calibrated_magnification>
               <specimen_holder_model>GATAN LIQUID NITROGEN</specimen_holder_model>
               <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">7.0</sampling_interval>
                     </digitization_details>
                     <number_real_images>210</number_real_images>
                     <average_electron_dose_per_image units="e/&#8491;^2">22</average_electron_dose_per_image>
                     <bits_per_pixel>12.</bits_per_pixel>
                  </image_recording>
               </image_recording_list>
               <specimen_holder>gatan 626 cryo holder</specimen_holder>
            </single_particle_microscopy>
         </microscopy_list>
         <singleparticle_processing image_processing_id="1">
            <ctf_correction>
               <details>each 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;">13.0</resolution>
               <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
               <software_list>
                  <software>
                     <name>AUTO3DEM</name>
                  </software>
               </software_list>
               <number_images_used>1800</number_images_used>
            </final_reconstruction>
            <final_two_d_classification>
               <number_classes>1</number_classes>
            </final_two_d_classification>
         </singleparticle_processing>
      </structure_determination>
   </structure_determination_list>
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      <file>emd_1580.map.gz</file>
      <symmetry>
         <space_group>1</space_group>
      </symmetry>
      <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
      <dimensions>
         <col>471</col>
         <row>471</row>
         <sec>471</sec>
      </dimensions>
      <origin>
         <col>0</col>
         <row>0</row>
         <sec>0</sec>
      </origin>
      <spacing>
         <x>471</x>
         <y>471</y>
         <z>471</z>
      </spacing>
      <cell>
         <a units="&#8491;">1997.04</a>
         <b units="&#8491;">1997.04</b>
         <c units="&#8491;">1997.04</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>-10.8142</minimum>
         <maximum>23.1188</maximum>
         <average>1.86893</average>
         <std>3.8831</std>
      </statistics>
      <pixel_spacing>
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         <y units="&#8491;">4.24</y>
         <z units="&#8491;">4.24</z>
      </pixel_spacing>
      <contour_list>
         <contour primary="true">
            <level>2.01</level>
            <source>AUTHOR</source>
         </contour>
      </contour_list>
      <annotation_details>Chilo Iridescent virus at 13 angstrom resolution</annotation_details>
      <details>::::EMDATABANK.org::::EMD-1580::::</details>
   </map>
</emd>