<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" emdb_id="EMD-2296" 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>2013-01-23</deposition>
         <header_release>2013-02-27</header_release>
         <map_release>2013-05-15</map_release>
         <update>2013-05-15</update>
      </key_dates>
      <title>The 14 A Cryo-EM structure of Dengue virus at 37C</title>
      <authors_list>
         <author>Fibriansah G</author>
         <author>Ng TS</author>
         <author>Kostyuchenko VA</author>
         <author>Lee S</author>
         <author>Wang J</author>
         <author>Lok SM</author>
      </authors_list>
      <keywords>dengue, breathing structure, dynamic structure</keywords>
   </admin>
   <crossreferences>
      <citation_list>
         <primary_citation>
            <journal_citation published="true">
               <author order="1">Fibriansah G</author>
               <author order="2">Ng TS</author>
               <author order="3">Kostyuchenko VA</author>
               <author order="4">Lee J</author>
               <author order="5">Lee S</author>
               <author order="6">Wang J</author>
               <author order="7">Lok SM</author>
               <title>Structural changes of dengue virus when exposed to 37oC.</title>
               <journal>J.VIROL.</journal>
               <volume>87</volume>
               <first_page>7585</first_page>
               <last_page>7592</last_page>
               <year>2013</year>
               <external_references type="PUBMED">23637405</external_references>
               <external_references type="DOI">doi:10.1128/JVI.00757-13</external_references>
            </journal_citation>
         </primary_citation>
      </citation_list>
      <pdb_list>
         <pdb_reference>
            <pdb_id>3zko</pdb_id>
            <relationship>
               <in_frame>FULLOVERLAP</in_frame>
            </relationship>
         </pdb_reference>
      </pdb_list>
   </crossreferences>
   <sample>
      <name>Dengue Virus 2</name>
      <supramolecule_list>
         <sample_supramolecule supramolecule_id="1000">
            <name>Dengue Virus 2</name>
            <oligomeric_state>full dengue virion</oligomeric_state>
            <number_unique_components>1</number_unique_components>
         </sample_supramolecule>
         <virus_supramolecule supramolecule_id="1">
            <name>Dengue virus 2</name>
            <sci_species_name ncbi="11060">Dengue virus 2</sci_species_name>
            <sci_species_strain>New Guinea C</sci_species_strain>
            <natural_host database="NCBI">
               <organism ncbi="9606">Homo sapiens</organism>
               <synonym_organism>VERTEBRATES</synonym_organism>
            </natural_host>
            <host_system database="NCBI">
               <recombinant_organism ncbi="7160">Aedes albopictus</recombinant_organism>
               <recombinant_cell>C6/36</recombinant_cell>
            </host_system>
            <virus_type>VIRION</virus_type>
            <virus_isolate>STRAIN</virus_isolate>
            <virus_enveloped>true</virus_enveloped>
            <virus_empty>false</virus_empty>
         </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>8.0</ph>
                  <details>10 mM Tris-HCl, 120 mM NaCl, 1 mM EDTA</details>
               </buffer>
               <grid>
                  <details>lacey carbon grid, layered with ultra thin carbon</details>
               </grid>
               <vitrification>
                  <cryogen_name>ETHANE</cryogen_name>
                  <chamber_humidity units="percentage">100</chamber_humidity>
                  <instrument>FEI VITROBOT MARK IV</instrument>
                  <method>2.5 microlitres virus sample was added per grid and blotted with filter paper for 2.5 s before plunging</method>
               </vitrification>
            </single_particle_preparation>
         </specimen_preparation_list>
         <microscopy_list>
            <single_particle_microscopy microscopy_id="1">
               <microscope>FEI TITAN KRIOS</microscope>
               <illumination_mode>SPOT SCAN</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">2.7</nominal_cs>
               <nominal_defocus_min units="&#181;m">1.5</nominal_defocus_min>
               <nominal_defocus_max units="&#181;m">3.0</nominal_defocus_max>
               <nominal_magnification>47000.0</nominal_magnification>
               <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
               <temperature>
                  <temperature_average units="K">100</temperature_average>
               </temperature>
               <date>2011-11-21</date>
               <image_recording_list>
                  <image_recording>
                     <film_or_detector_model category="CCD">GENERIC GATAN</film_or_detector_model>
                     <number_real_images>302</number_real_images>
                     <average_electron_dose_per_image units="e/&#8491;^2">18.5</average_electron_dose_per_image>
                  </image_recording>
               </image_recording_list>
            </single_particle_microscopy>
         </microscopy_list>
         <singleparticle_processing image_processing_id="1">
            <details>The particles were selected manually</details>
            <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;">13.7</resolution>
               <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
               <software_list>
                  <software>
                     <name>EMAN, EMAN2, MPSA</name>
                  </software>
               </software_list>
               <details>The particles were selected manually.</details>
               <number_images_used>5861</number_images_used>
            </final_reconstruction>
         </singleparticle_processing>
      </structure_determination>
   </structure_determination_list>
   <map format="CCP4" size_kbytes="488283">
      <file>emd_2296.map.gz</file>
      <symmetry>
         <space_group>1</space_group>
      </symmetry>
      <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
      <dimensions>
         <col>500</col>
         <row>500</row>
         <sec>500</sec>
      </dimensions>
      <origin>
         <col>-250</col>
         <row>-250</row>
         <sec>-250</sec>
      </origin>
      <spacing>
         <x>500</x>
         <y>500</y>
         <z>500</z>
      </spacing>
      <cell>
         <a units="&#8491;">950.0</a>
         <b units="&#8491;">950.0</b>
         <c units="&#8491;">950.0</c>
         <alpha units="deg">90.0</alpha>
         <beta units="deg">90.0</beta>
         <gamma units="deg">90.0</gamma>
      </cell>
      <axis_order>
         <fast>X</fast>
         <medium>Y</medium>
         <slow>Z</slow>
      </axis_order>
      <statistics>
         <minimum>-6.12860346</minimum>
         <maximum>10.112843509999999</maximum>
         <average>0.0363888</average>
         <std>0.99221563</std>
      </statistics>
      <pixel_spacing>
         <x units="&#8491;">1.9</x>
         <y units="&#8491;">1.9</y>
         <z units="&#8491;">1.9</z>
      </pixel_spacing>
      <contour_list>
         <contour primary="true">
            <level>2.0</level>
            <source>AUTHOR</source>
         </contour>
      </contour_list>
      <annotation_details>Reconstruction of one particles class in the "breathing" dengue virus particles</annotation_details>
      <details>::::EMDATABANK.org::::EMD-2296::::</details>
   </map>
   <interpretation>
      <modelling_list>
         <modelling>
            <initial_model>
               <access_code>1P58</access_code>
               <chain>
                  <chain_id>A</chain_id>
               </chain>
               <chain>
                  <chain_id>B</chain_id>
               </chain>
               <chain>
                  <chain_id>C</chain_id>
               </chain>
            </initial_model>
            <refinement_protocol>RIGID BODY FIT</refinement_protocol>
            <software_list>
               <software>
                  <name>Chimera</name>
               </software>
            </software_list>
            <details>Individual envelope protein molecules were fitted separately by manual docking using program O</details>
            <target_criteria>Correlation</target_criteria>
            <refinement_space>REAL</refinement_space>
         </modelling>
      </modelling_list>
      <figure_list>
         <figure>
            <file>emd_2296.png</file>
         </figure>
      </figure_list>
   </interpretation>
</emd>