<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" emdb_id="EMD-1692" 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>2010-01-25</deposition>
         <header_release>2010-04-09</header_release>
         <map_release>2011-01-28</map_release>
         <update>2012-10-10</update>
      </key_dates>
      <title>Cryo-EM reconstruction of Phage Gifsy-2 darker procapsid</title>
      <authors_list>
         <author>Effantin G</author>
         <author>Figueroa-Bossi N</author>
         <author>Schoehn G</author>
         <author>Bossi L</author>
         <author>Conway JF</author>
      </authors_list>
      <keywords>Bacteriophage,Gifsy-2,capsid</keywords>
   </admin>
   <crossreferences>
      <citation_list>
         <primary_citation>
            <journal_citation published="true">
               <author order="1">Effantin G</author>
               <author order="2">Figueroa-Bossi N</author>
               <author order="3">Schoehn G</author>
               <author order="4">Bossi L</author>
               <author order="5">Conway JF</author>
               <title>The tripartite capsid gene of Salmonella phage Gifsy-2 yields a capsid assembly pathway engaging features from HK97 and lambda.</title>
               <journal>VIROLOGY</journal>
               <volume>402</volume>
               <first_page>355</first_page>
               <last_page>365</last_page>
               <year>2010</year>
               <external_references type="PUBMED">20427067</external_references>
               <external_references type="DOI">doi:10.1016/j.virol.2010.03.041</external_references>
            </journal_citation>
         </primary_citation>
      </citation_list>
   </crossreferences>
   <sample>
      <name>Bacteriophage Gifsy-2 procapsid purified from Salmonella Typhimurium</name>
      <supramolecule_list>
         <sample_supramolecule supramolecule_id="1000">
            <name>Bacteriophage Gifsy-2 procapsid purified from Salmonella Typhimurium</name>
            <oligomeric_state>1</oligomeric_state>
            <number_unique_components>1</number_unique_components>
         </sample_supramolecule>
         <virus_supramolecule supramolecule_id="1">
            <name synonym="Gifsy-2">Phage Gifsy-2</name>
            <sci_species_name ncbi="129862">Phage Gifsy-2</sci_species_name>
            <natural_host database="NCBI">
               <organism ncbi="90371">Salmonella enterica subsp. enterica serovar Typhimurium</organism>
               <synonym_organism>BACTERIA(EUBACTERIA)</synonym_organism>
            </natural_host>
            <host_system database="NCBI">
               </host_system>
            <virus_shell shell_id="1">
               <diameter units="&#8491;">570</diameter>
               <triangulation>7</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>Gifsy-2</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>7.5</ph>
                  <details>10 mM Tris-HCl pH7.5, 10 mM MgSO4</details>
               </buffer>
               <grid>
                  <details>300 mesh copper grid</details>
               </grid>
               <vitrification>
                  <cryogen_name>ETHANE</cryogen_name>
                  <instrument>HOMEMADE PLUNGER</instrument>
                  <details>Vitrification instrument: Home made manual plunger</details>
               </vitrification>
            </single_particle_preparation>
         </specimen_preparation_list>
         <microscopy_list>
            <single_particle_microscopy microscopy_id="1">
               <microscope>FEI/PHILIPS CM200T</microscope>
               <illumination_mode>SPOT SCAN</illumination_mode>
               <imaging_mode>BRIGHT FIELD</imaging_mode>
               <electron_source>LAB6</electron_source>
               <acceleration_voltage units="kV">200</acceleration_voltage>
               <nominal_cs units="mm">2</nominal_cs>
               <nominal_defocus_min units="&#181;m">1.0</nominal_defocus_min>
               <nominal_defocus_max units="&#181;m">4.0</nominal_defocus_max>
               <nominal_magnification>38000.0</nominal_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">1.84</sampling_interval>
                     </digitization_details>
                     <number_real_images>51</number_real_images>
                  </image_recording>
               </image_recording_list>
               <specimen_holder>Eucentric</specimen_holder>
            </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>
               <algorithm>OTHER</algorithm>
               <resolution res_type="BY AUTHOR" units="&#8491;">25.6</resolution>
               <resolution_method>FSC 0.33 CUT-OFF</resolution_method>
               <software_list>
                  <software>
                     <name>pft - em3dr</name>
                  </software>
               </software_list>
               <number_images_used>56</number_images_used>
            </final_reconstruction>
         </singleparticle_processing>
      </structure_determination>
   </structure_determination_list>
   <map format="CCP4" size_kbytes="99737">
      <file>emd_1692.map.gz</file>
      <symmetry>
         <space_group>1</space_group>
      </symmetry>
      <data_type>IMAGE STORED AS SIGNED INTEGER (2 BYTES)</data_type>
      <dimensions>
         <col>371</col>
         <row>371</row>
         <sec>371</sec>
      </dimensions>
      <origin>
         <col>-185</col>
         <row>-185</row>
         <sec>-2</sec>
      </origin>
      <spacing>
         <x>371</x>
         <y>371</y>
         <z>371</z>
      </spacing>
      <cell>
         <a units="&#8491;">683.382</a>
         <b units="&#8491;">683.382</b>
         <c units="&#8491;">683.382</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>-735.0</minimum>
         <maximum>932.0</maximum>
         <average>12.5459</average>
         <std>138.436000000000007</std>
      </statistics>
      <pixel_spacing>
         <x units="&#8491;">1.842</x>
         <y units="&#8491;">1.842</y>
         <z units="&#8491;">1.842</z>
      </pixel_spacing>
      <contour_list>
         <contour primary="true">
            <level>173.0</level>
            <source>AUTHOR</source>
         </contour>
      </contour_list>
      <annotation_details>Gifsy-2 darker procapsid</annotation_details>
      <details>::::EMDATABANK.org::::EMD-1692::::</details>
   </map>
</emd>