<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" emdb_id="EMD-1679" 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>2010-01-12</deposition>
         <header_release>2010-03-10</header_release>
         <map_release>2010-03-11</map_release>
         <update>2011-09-09</update>
      </key_dates>
      <title>Characterization of the extremophilic, archaeal virus STIV2</title>
      <authors_list>
         <author>Happonen LJ</author>
         <author>Redder P</author>
         <author>Peng X</author>
         <author>Reigstad LJ</author>
         <author>Prangishvili D</author>
         <author>Butcher SJ</author>
      </authors_list>
      <keywords>Archaeal, virus, icosahedral, extremophilic</keywords>
   </admin>
   <crossreferences>
      <citation_list>
         <primary_citation>
            <journal_citation published="true">
               <author order="1">Happonen LJ</author>
               <author order="2">Redder P</author>
               <author order="3">Peng X</author>
               <author order="4">Reigstad LJ</author>
               <author order="5">Prangishvili D</author>
               <author order="6">Butcher SJ</author>
               <title>Familial relationships in hyperthermo- and acidophilic archaeal viruses.</title>
               <journal>J.VIROL.</journal>
               <volume>84</volume>
               <first_page>4747</first_page>
               <last_page>4754</last_page>
               <year>2010</year>
               <external_references type="PUBMED">20164227</external_references>
               <external_references type="DOI">doi:10.1128/JVI.02156-09</external_references>
            </journal_citation>
         </primary_citation>
      </citation_list>
   </crossreferences>
   <sample>
      <name>STIV2 virus</name>
      <supramolecule_list>
         <sample_supramolecule supramolecule_id="1000">
            <name>STIV2 virus</name>
            <number_unique_components>1</number_unique_components>
         </sample_supramolecule>
         <virus_supramolecule supramolecule_id="1">
            <name synonym="STIV2">Sulfolobus turreted icosahedral virus 2</name>
            <sci_species_name ncbi="754004">Sulfolobus turreted icosahedral virus 2</sci_species_name>
            <natural_host database="NCBI">
               <organism ncbi="43080">Sulfolobus islandicus</organism>
               <synonym_organism>ARCHAEA</synonym_organism>
            </natural_host>
            <host_system database="NCBI">
               </host_system>
            <virus_shell shell_id="1">
               <diameter units="&#8491;">710</diameter>
               <triangulation>31</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>STIV2</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">
               <buffer>
                  <ph>3.5</ph>
                  <details>50 mM sodium citrate, pH 3.5</details>
               </buffer>
               <staining>
                  <type>NEGATIVE</type>
                  <details>Vitrified. Grids were blotted for roughly one second before being plunged into liquid ethane.</details>
               </staining>
               <grid>
                  <details>Quantifoil-grids</details>
               </grid>
               <vitrification>
                  <cryogen_name>ETHANE</cryogen_name>
                  <instrument>HOMEMADE PLUNGER</instrument>
                  <details>Vitrification instrument: Guillotine</details>
                  <method>A small vial of ethane is placed inside a larger liquid nitrogen reservoir. The grid holding 3 microliters of the sample is held in place at the bottom of a plunger by the means of fine tweezers. When the liquid ethane is ready, a piece of filter paper is then pressed against the sample to blot off excess buffer, sufficient to leave a thin layer on the grid. The filter paper is removed, and the plunger is allowed to drop into the liquid ethane. Once the grid enters the liquid ethane, the sample is rapidly frozen, and the grid is transferred under liquid nitrogen to a storage box immersed in liquid nitrogen for later use in the microscope.</method>
               </vitrification>
            </single_particle_preparation>
         </specimen_preparation_list>
         <microscopy_list>
            <single_particle_microscopy microscopy_id="1">
               <microscope>FEI TECNAI F20</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">2.0</nominal_cs>
               <nominal_defocus_min units="&#181;m">0.5</nominal_defocus_min>
               <nominal_defocus_max units="&#181;m">5.2</nominal_defocus_max>
               <nominal_magnification>68000.0</nominal_magnification>
               <calibrated_magnification>66400.0</calibrated_magnification>
               <specimen_holder_model>GATAN LIQUID NITROGEN</specimen_holder_model>
               <details>Low dose conditions</details>
               <image_recording_list>
                  <image_recording>
                     <film_or_detector_model category="CCD">GATAN ULTRASCAN 4000 (4k x 4k)</film_or_detector_model>
                     <digitization_details>
                        <sampling_interval units="&#181;m">4.42</sampling_interval>
                     </digitization_details>
                     <number_real_images>358</number_real_images>
                     <average_electron_dose_per_image units="e/&#8491;^2">18</average_electron_dose_per_image>
                  </image_recording>
               </image_recording_list>
               <specimen_holder>Side entry liquid nitrogen-cooled side entry 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;">20.0</resolution>
               <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
               <software_list>
                  <software>
                     <name>PFT, POR, EM3DR2, P3DR</name>
                  </software>
               </software_list>
               <number_images_used>713</number_images_used>
            </final_reconstruction>
         </singleparticle_processing>
      </structure_determination>
   </structure_determination_list>
   <map format="CCP4" size_kbytes="136587">
      <file>emd_1679.map.gz</file>
      <symmetry>
         <space_group>1</space_group>
      </symmetry>
      <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
      <dimensions>
         <col>327</col>
         <row>327</row>
         <sec>327</sec>
      </dimensions>
      <origin>
         <col>0</col>
         <row>0</row>
         <sec>0</sec>
      </origin>
      <spacing>
         <x>327</x>
         <y>327</y>
         <z>327</z>
      </spacing>
      <cell>
         <a units="&#8491;">327.08</a>
         <b units="&#8491;">327.08</b>
         <c units="&#8491;">327.08</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>-2959.329999999999927</minimum>
         <maximum>4678.529999999999745</maximum>
         <average>0.000000058474</average>
         <std>480.0</std>
      </statistics>
      <pixel_spacing>
         <x units="&#8491;">4.42</x>
         <y units="&#8491;">4.42</y>
         <z units="&#8491;">4.42</z>
      </pixel_spacing>
      <contour_list>
         <contour primary="true">
            <level>960.0</level>
            <source>AUTHOR</source>
         </contour>
      </contour_list>
      <annotation_details>This is a 20 A resolution cryo-EM reconstruction of the archaeal virus STIV2</annotation_details>
      <details>::::EMDATABANK.org::::EMD-1679::::</details>
   </map>
</emd>