<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" emdb_id="EMD-2338" 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>2013-03-20</deposition>
         <header_release>2013-04-17</header_release>
         <map_release>2013-07-24</map_release>
         <update>2013-07-24</update>
      </key_dates>
      <title>The baseplate of mycobacteriophage Araucaria</title>
      <authors_list>
         <author>Sassi M</author>
         <author>Bebeacua C</author>
         <author>Drancourt M</author>
         <author>Cambillau C</author>
      </authors_list>
      <keywords>mycobacteriophage, Araucaria, single-particle, Mycobacterium abscessus subsp. bolletii, Siphoviridae, electron microscopy, mycobacteria.</keywords>
   </admin>
   <crossreferences>
      <citation_list>
         <primary_citation>
            <journal_citation published="true">
               <author order="1">Sassi M</author>
               <author order="2">Bebeacua C</author>
               <author order="3">Drancourt M</author>
               <author order="4">Cambillau C</author>
               <title>The first structure of a mycobacteriophage, the Mycobacterium abscessus subsp. bolletii phage Araucaria.</title>
               <journal>J.VIROL.</journal>
               <volume>87</volume>
               <first_page>8099</first_page>
               <last_page>8109</last_page>
               <year>2013</year>
               <external_references type="PUBMED">23678183</external_references>
               <external_references type="DOI">doi:10.1128/JVI.01209-13</external_references>
            </journal_citation>
         </primary_citation>
      </citation_list>
   </crossreferences>
   <sample>
      <name>Mycobacteriophage Araucaria Baseplate</name>
      <supramolecule_list>
         <sample_supramolecule supramolecule_id="1000">
            <name>Mycobacteriophage Araucaria Baseplate</name>
            <details>Baseplate particles were selected from a sample containing whole phages.</details>
            <oligomeric_state>C6</oligomeric_state>
            <number_unique_components>1</number_unique_components>
         </sample_supramolecule>
         <virus_supramolecule supramolecule_id="1">
            <name synonym="Araucaria">Mycobacteriophage Araucaria</name>
            <sci_species_name>Mycobacteriophage Araucaria</sci_species_name>
            <natural_host database="NCBI">
               <organism ncbi="319705">Mycobacterium abscessus subsp. bolletii</organism>
               <strain>CIP108541T</strain>
               <synonym_organism>BACTERIA(EUBACTERIA)</synonym_organism>
            </natural_host>
            <host_system database="NCBI">
               </host_system>
            <virus_shell shell_id="1">
               <name>Capsid T7</name>
               <diameter units="&#8491;">600</diameter>
               <triangulation>7</triangulation>
            </virus_shell>
            <virus_type>VIRION</virus_type>
            <virus_isolate>SPECIES</virus_isolate>
            <virus_enveloped>false</virus_enveloped>
            <virus_empty>false</virus_empty>
            <syn_species_name>Araucaria</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>7.0</ph>
                  <details>PBS Buffer</details>
               </buffer>
               <staining>
                  <type>NEGATIVE</type>
                  <details>Grids with adsorbed viral particles were stained with 2% uranyl acetate for 20 seconds.</details>
               </staining>
               <grid>
                  <details>300 copper mesh grids with a film of colodion and carbon</details>
               </grid>
               <vitrification>
                  <cryogen_name>NONE</cryogen_name>
                  <instrument>OTHER</instrument>
               </vitrification>
            </single_particle_preparation>
         </specimen_preparation_list>
         <microscopy_list>
            <single_particle_microscopy microscopy_id="1">
               <microscope>FEI TECNAI 12</microscope>
               <illumination_mode>FLOOD BEAM</illumination_mode>
               <imaging_mode>BRIGHT FIELD</imaging_mode>
               <electron_source>LAB6</electron_source>
               <acceleration_voltage units="kV">120</acceleration_voltage>
               <nominal_cs units="mm">2</nominal_cs>
               <nominal_defocus_min units="&#181;m">1.5</nominal_defocus_min>
               <nominal_defocus_max units="&#181;m">1.5</nominal_defocus_max>
               <nominal_magnification>48500.0</nominal_magnification>
               <calibrated_magnification>48500.0</calibrated_magnification>
               <specimen_holder_model>SIDE ENTRY, EUCENTRIC</specimen_holder_model>
               <alignment_procedure>
                  <legacy>
                     <astigmatism>Objective lens astigmatism was corrected at 150,000 times magnification</astigmatism>
                  </legacy>
               </alignment_procedure>
               <date>2012-07-01</date>
               <image_recording_list>
                  <image_recording>
                     <film_or_detector_model category="CCD">GENERIC CCD (2k x 2k)</film_or_detector_model>
                     <number_real_images>1500</number_real_images>
                     <average_electron_dose_per_image units="e/&#8491;^2">10</average_electron_dose_per_image>
                  </image_recording>
               </image_recording_list>
               <specimen_holder>Room temperature holder</specimen_holder>
            </single_particle_microscopy>
         </microscopy_list>
         <singleparticle_processing image_processing_id="1">
            <details>Particles were processed using a Maximum Likelihood approach.</details>
            <final_reconstruction>
               <applied_symmetry>
                  <point_group>C6</point_group>
               </applied_symmetry>
               <algorithm>OTHER</algorithm>
               <resolution res_type="BY AUTHOR" units="&#8491;">26.0</resolution>
               <resolution_method>OTHER</resolution_method>
               <software_list>
                  <software>
                     <name>EMAN2, Spider, Xmipp</name>
                  </software>
               </software_list>
               <number_images_used>6460</number_images_used>
            </final_reconstruction>
            <final_angle_assignment>
               <details>C6</details>
            </final_angle_assignment>
         </singleparticle_processing>
      </structure_determination>
   </structure_determination_list>
   <map format="CCP4" size_kbytes="3908">
      <file>emd_2338.map.gz</file>
      <symmetry>
         <space_group>1</space_group>
      </symmetry>
      <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
      <dimensions>
         <col>100</col>
         <row>100</row>
         <sec>100</sec>
      </dimensions>
      <origin>
         <col>0</col>
         <row>0</row>
         <sec>0</sec>
      </origin>
      <spacing>
         <x>100</x>
         <y>100</y>
         <z>100</z>
      </spacing>
      <cell>
         <a units="&#8491;">494.99997</a>
         <b units="&#8491;">494.99997</b>
         <c units="&#8491;">494.99997</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>-0.21920949</minimum>
         <maximum>0.35790157</maximum>
         <average>0.00307062</average>
         <std>0.02232647</std>
      </statistics>
      <pixel_spacing>
         <x units="&#8491;">4.95</x>
         <y units="&#8491;">4.95</y>
         <z units="&#8491;">4.95</z>
      </pixel_spacing>
      <contour_list>
         <contour primary="true">
            <level>0.03</level>
            <source>AUTHOR</source>
         </contour>
      </contour_list>
      <annotation_details>Reconstruction of the Araucaria baseplate</annotation_details>
      <details>::::EMDATABANK.org::::EMD-2338::::</details>
   </map>
   <interpretation>
      <modelling_list>
         <modelling>
            <initial_model>
               <access_code>2X8K</access_code>
            </initial_model>
            <refinement_protocol>RIGID BODY FIT</refinement_protocol>
            <software_list>
               <software>
                  <name>Chimera</name>
               </software>
            </software_list>
            <details>Atomic coordinates were manually fitted and automatically refined.</details>
            <refinement_space>REAL</refinement_space>
         </modelling>
      </modelling_list>
   </interpretation>
</emd>