<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" emdb_id="EMD-1351" 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>2007-04-02</deposition>
         <header_release>2007-04-02</header_release>
         <map_release>2008-05-17</map_release>
         <update>2012-10-24</update>
      </key_dates>
      <title>Structure and host cell interaction of SH1, a membrane-containing, halophilic euryarchaeal virus</title>
      <authors_list>
         <author>Jaalinoja HT</author>
         <author>Roine E</author>
         <author>Kivela H</author>
         <author>Butcher SJ</author>
      </authors_list>
      <keywords>
         </keywords>
   </admin>
   <crossreferences>
      <citation_list>
         <primary_citation>
            <journal_citation published="true">
               <author order="1">Jaalinoja HT</author>
               <author order="2">Roine E</author>
               <author order="3">Laurinmaki P</author>
               <author order="4">Kivela HM</author>
               <author order="5">Bamford DH</author>
               <author order="6">Butcher SJ</author>
               <title>Structure and host-cell interaction of SH1, a membrane-containing, halophilic euryarchaeal virus.</title>
               <journal>PROC.NAT.ACAD.SCI.USA</journal>
               <volume>105</volume>
               <first_page>8008</first_page>
               <last_page>8013</last_page>
               <year>2008</year>
               <external_references type="PUBMED">18515426</external_references>
               <external_references type="DOI">doi:10.1073/pnas.0801758105</external_references>
            </journal_citation>
         </primary_citation>
      </citation_list>
   </crossreferences>
   <sample>
      <name>SH1 subviral particle VP36-</name>
      <supramolecule_list>
         <sample_supramolecule supramolecule_id="1000">
            <name>SH1 subviral particle VP36-</name>
            <number_unique_components>1</number_unique_components>
         </sample_supramolecule>
         <virus_supramolecule supramolecule_id="1">
            <name synonym="SH1 subviral particle VP36-">Haloarcula phage SH1</name>
            <sci_species_name ncbi="326574">Haloarcula phage SH1</sci_species_name>
            <natural_host database="NCBI">
               <organism ncbi="51589">Haloarcula hispanica</organism>
               <synonym_organism>ARCHAEA</synonym_organism>
            </natural_host>
            <host_system database="NCBI">
               </host_system>
            <virus_shell shell_id="1">
               <name>capsid</name>
               <diameter units="&#8491;">800</diameter>
               <triangulation>28</triangulation>
            </virus_shell>
            <virus_type>VIRUS-LIKE PARTICLE</virus_type>
            <virus_isolate>STRAIN</virus_isolate>
            <virus_enveloped>false</virus_enveloped>
            <virus_empty>false</virus_empty>
            <syn_species_name>SH1 subviral particle VP36-</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>7.2</ph>
                  <details>40 mM Tris-HCl pH 7.2, 0.75 M Na2SO4, 40 mM MgSO4</details>
               </buffer>
               <grid>
                  <details>400 mesh copper grid, Quantifoil R2/2 holey</details>
               </grid>
               <vitrification>
                  <cryogen_name>ETHANE</cryogen_name>
                  <chamber_temperature units="K">90</chamber_temperature>
                  <instrument>HOMEMADE PLUNGER</instrument>
                  <details>Vitrification instrument: EMBL design</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">0.733</nominal_defocus_min>
               <nominal_defocus_max units="&#181;m">3.484</nominal_defocus_max>
               <nominal_magnification>50000.0</nominal_magnification>
               <calibrated_magnification>49300.0</calibrated_magnification>
               <specimen_holder_model>GATAN LIQUID NITROGEN</specimen_holder_model>
               <temperature>
                  <temperature_min units="K">90</temperature_min>
                  <temperature_max units="K">94</temperature_max>
                  <temperature_average units="K">93</temperature_average>
               </temperature>
               <details>Low dose conditions.</details>
               <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</sampling_interval>
                     </digitization_details>
                     <number_real_images>58</number_real_images>
                  </image_recording>
               </image_recording_list>
               <specimen_holder>Side entry liquid nitrogen-cooled cryo specimen holder</specimen_holder>
               <tilt_angle_min>0</tilt_angle_min>
               <tilt_angle_max>0</tilt_angle_max>
            </single_particle_microscopy>
         </microscopy_list>
         <singleparticle_processing image_processing_id="1">
            <ctf_correction>
               <details>Each particle, wiener factor 0.2</details>
            </ctf_correction>
            <final_reconstruction>
               <applied_symmetry>
                  <point_group>I</point_group>
               </applied_symmetry>
               <algorithm>OTHER</algorithm>
               <resolution res_type="BY AUTHOR" units="&#8491;">10.5</resolution>
               <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
               <software_list>
                  <software>
                     <name>pft2, em3dr2, POR, P3DR</name>
                  </software>
               </software_list>
               <number_images_used>985</number_images_used>
            </final_reconstruction>
         </singleparticle_processing>
      </structure_determination>
   </structure_determination_list>
   <map format="CCP4" size_kbytes="145741">
      <file>emd_1351.map.gz</file>
      <symmetry>
         <space_group>1</space_group>
      </symmetry>
      <data_type>IMAGE STORED AS SIGNED INTEGER (2 BYTES)</data_type>
      <dimensions>
         <col>421</col>
         <row>421</row>
         <sec>421</sec>
      </dimensions>
      <origin>
         <col>0</col>
         <row>0</row>
         <sec>0</sec>
      </origin>
      <spacing>
         <x>421</x>
         <y>421</y>
         <z>421</z>
      </spacing>
      <cell>
         <a units="&#8491;">1178.8</a>
         <b units="&#8491;">1178.8</b>
         <c units="&#8491;">1178.8</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>-15891.0</minimum>
         <maximum>32443.0</maximum>
         <average>304.646000000000015</average>
         <std>3311.019999999999982</std>
      </statistics>
      <pixel_spacing>
         <x units="&#8491;">2.8</x>
         <y units="&#8491;">2.8</y>
         <z units="&#8491;">2.8</z>
      </pixel_spacing>
      <contour_list>
         <contour primary="true">
            <level>5640.0</level>
         </contour>
      </contour_list>
      <annotation_details>CryoEM reconstruction of SH1 subviral particle VP36-.</annotation_details>
      <details>::::EMDATABANK.org::::EMD-1351::::</details>
   </map>
</emd>