<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" emdb_id="EMD-2818" 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>2014-11-14</deposition>
         <header_release>2014-12-10</header_release>
         <map_release>2014-12-10</map_release>
         <update>2016-02-17</update>
      </key_dates>
      <title>Dengue virus serotype 2 with Fab fragments of human antibody B7</title>
      <authors_list>
         <author>Dejnirattisai W</author>
         <author>Wongwiwat W</author>
         <author>Supasa S</author>
         <author>Zhang X</author>
         <author>Dai X</author>
         <author>Rouvinsky A</author>
         <author>Jumnainsong A</author>
         <author>Edwards C</author>
         <author>Quyen NT</author>
         <author>Duangchinda T</author>
         <author>Grimes JM</author>
         <author>Tsai WY</author>
         <author>Lai CY</author>
         <author>Wang WK</author>
         <author>Malasit P</author>
         <author>Farrar J</author>
         <author>Simmons CP</author>
         <author>Zhou ZH</author>
         <author>Rey FA</author>
         <author>Mongkolsapaya J</author>
         <author>Screaton GR</author>
      </authors_list>
      <keywords>dengue virus, human monoclonal antibody, potent broad neutralization, E-dimer Dependent epitope</keywords>
   </admin>
   <crossreferences>
      <citation_list>
         <primary_citation>
            <journal_citation published="true">
               <author order="1">Dejnirattisai W</author>
               <author order="2">Wongwiwat W</author>
               <author order="3">Supasa S</author>
               <author order="4">Zhang X</author>
               <author order="5">Dai X</author>
               <author order="6">Rouvinski A</author>
               <author order="7">Rouvinsky A</author>
               <author order="8">Jumnainsong A</author>
               <author order="9">Edwards C</author>
               <author order="10">Quyen NT</author>
               <author order="11">Duangchinda T</author>
               <author order="12">Grimes JM</author>
               <author order="13">Tsai WY</author>
               <author order="14">Lai CY</author>
               <author order="15">Wang WK</author>
               <author order="16">Malasit P</author>
               <author order="17">Farrar J</author>
               <author order="18">Simmons CP</author>
               <author order="19">Zhou ZH</author>
               <author order="20">Rey FA</author>
               <author order="21">Mongkolsapaya J</author>
               <author order="22">Screaton GR</author>
               <title>A new class of highly potent, broadly neutralizing antibodies isolated from viremic patients infected with dengue virus.</title>
               <journal>NAT.IMMUNOL.</journal>
               <volume>16</volume>
               <first_page>170</first_page>
               <last_page>177</last_page>
               <year>2015</year>
               <external_references type="PUBMED">25501631</external_references>
               <external_references type="DOI">doi:10.1038/ni.3058</external_references>
            </journal_citation>
         </primary_citation>
         <secondary_citation>
            <journal_citation published="false">
               <author order="1">Rouvinski A</author>
               <author order="2">Guardado-Calvo P</author>
               <author order="3">Barba-Spaeth G</author>
               <author order="4">Duquerroy S</author>
               <author order="5">Vaney MC</author>
               <author order="6">Kikuti CM</author>
               <author order="7">Navarro Sanchez E</author>
               <author order="8">Dejnirattisai W</author>
               <author order="9">Wongwiwat W</author>
               <author order="10">Haouz A</author>
               <author order="11">Girard-Blanc C</author>
               <author order="12">Petres S</author>
               <author order="13">England P</author>
               <author order="14">Supasa S</author>
               <author order="15">Shepard WE</author>
               <author order="16">Duangchinda T</author>
               <author order="17">Siridechadilok B</author>
               <author order="18">Despres P</author>
               <author order="19">Arenzana-Seisdedos F</author>
               <author order="20">Dussart P</author>
               <author order="21">Mongkolsapaya J</author>
               <author order="22">Screaton GR</author>
               <author order="23">Rey FA</author>
               <title>Recognition determinants of broadly neutralizing human antibodies against dengue viruses</title>
               <journal>NATURE</journal>
            </journal_citation>
         </secondary_citation>
      </citation_list>
   </crossreferences>
   <sample>
      <name>Fab Fragment of human antibody to Dengue 2 virus</name>
      <supramolecule_list>
         <sample_supramolecule supramolecule_id="1000">
            <name>Fab Fragment of human antibody to Dengue 2 virus</name>
            <number_unique_components>2</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>NGC</sci_species_strain>
            <natural_host database="NCBI">
               <organism ncbi="7159">Aedes aegypti</organism>
               <synonym_organism>INVERTEBRATES</synonym_organism>
            </natural_host>
            <host_system database="NCBI">
               </host_system>
            <virus_shell shell_id="1">
               <diameter units="&#8491;">500</diameter>
               <triangulation>3</triangulation>
            </virus_shell>
            <virus_type>VIRION</virus_type>
            <virus_isolate>STRAIN</virus_isolate>
            <virus_enveloped>true</virus_enveloped>
            <virus_empty>false</virus_empty>
         </virus_supramolecule>
      </supramolecule_list>
      <macromolecule_list>
         <protein_or_peptide macromolecule_id="1">
            <name>FAB</name>
            <natural_source database="NCBI">
               <organism ncbi="9606">Homo sapiens</organism>
               <synonym_organism>Human</synonym_organism>
            </natural_source>
            <recombinant_exp_flag>false</recombinant_exp_flag>
            <recombinant_expression database="NCBI">
               </recombinant_expression>
            <sequence>
               </sequence>
         </protein_or_peptide>
      </macromolecule_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>7.4</ph>
                  <details>PBS</details>
               </buffer>
               <grid>
                  <details>200 mesh quantifoil 2/2</details>
               </grid>
               <vitrification>
                  <cryogen_name>ETHANE</cryogen_name>
                  <chamber_humidity units="percentage">100</chamber_humidity>
                  <instrument>FEI VITROBOT MARK IV</instrument>
                  <method>Blot for 4 seconds 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>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">2.7</nominal_cs>
               <nominal_defocus_min units="&#181;m">0.2</nominal_defocus_min>
               <nominal_defocus_max units="&#181;m">3.5</nominal_defocus_max>
               <nominal_magnification>29000.0</nominal_magnification>
               <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
               <date>2014-06-09</date>
               <image_recording_list>
                  <image_recording>
                     <film_or_detector_model category="CCD">GATAN K2 (4k x 4k)</film_or_detector_model>
                     <digitization_details>
                        <sampling_interval units="&#181;m">5.0</sampling_interval>
                     </digitization_details>
                     <number_real_images>1000</number_real_images>
                     <average_electron_dose_per_image units="e/&#8491;^2">25</average_electron_dose_per_image>
                     <details>Every image is the average of 25 frames recorded by the direct electron detector</details>
                     <bits_per_pixel>32.</bits_per_pixel>
                  </image_recording>
               </image_recording_list>
               <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</details>
            </ctf_correction>
            <final_reconstruction>
               <applied_symmetry>
                  <point_group>I</point_group>
               </applied_symmetry>
               <algorithm>OTHER</algorithm>
               <resolution res_type="BY AUTHOR" units="&#8491;">10.24</resolution>
               <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
               <software_list>
                  <software>
                     <name>Relion, EMAN2</name>
                  </software>
               </software_list>
               <number_images_used>8000</number_images_used>
            </final_reconstruction>
         </singleparticle_processing>
      </structure_determination>
   </structure_determination_list>
   <map format="CCP4" size_kbytes="128001">
      <file>emd_2818.map.gz</file>
      <symmetry>
         <space_group>1</space_group>
      </symmetry>
      <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
      <dimensions>
         <col>320</col>
         <row>320</row>
         <sec>320</sec>
      </dimensions>
      <origin>
         <col>0</col>
         <row>0</row>
         <sec>0</sec>
      </origin>
      <spacing>
         <x>320</x>
         <y>320</y>
         <z>320</z>
      </spacing>
      <cell>
         <a units="&#8491;">819.19995</a>
         <b units="&#8491;">819.19995</b>
         <c units="&#8491;">819.19995</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>-8.33887768</minimum>
         <maximum>14.047575950000001</maximum>
         <average>0.00544979</average>
         <std>0.94821829</std>
      </statistics>
      <pixel_spacing>
         <x units="&#8491;">2.56</x>
         <y units="&#8491;">2.56</y>
         <z units="&#8491;">2.56</z>
      </pixel_spacing>
      <contour_list>
         <contour primary="true">
            <level>1.5</level>
            <source>AUTHOR</source>
         </contour>
      </contour_list>
      <annotation_details>Reconstruction of Dengue Virus Serotype 2 in complex with Human Antibody B7 Fab Fragment.</annotation_details>
      <details>::::EMDATABANK.org::::EMD-2818::::</details>
   </map>
   <interpretation>
      <modelling_list>
         <modelling>
            <initial_model>
               <access_code>3J27</access_code>
               <chain>
                  <chain_id>A</chain_id>
               </chain>
               <chain>
                  <chain_id>B</chain_id>
               </chain>
               <chain>
                  <chain_id>C</chain_id>
               </chain>
               <chain>
                  <chain_id>D</chain_id>
               </chain>
               <chain>
                  <chain_id>E</chain_id>
               </chain>
               <chain>
                  <chain_id>F</chain_id>
               </chain>
            </initial_model>
            <refinement_protocol>RIGID BODY FIT</refinement_protocol>
            <software_list>
               <software>
                  <name>UCSF Chimera</name>
               </software>
            </software_list>
            <target_criteria>cross coefficient</target_criteria>
            <refinement_space>REAL</refinement_space>
         </modelling>
      </modelling_list>
   </interpretation>
   <validation>
      <fsc_curve>
         <file>emd_2818_fsc.xml</file>
      </fsc_curve>
   </validation>
</emd>