<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" emdb_id="EMD-2462" 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>2013-09-11</deposition>
         <header_release>2013-09-25</header_release>
         <map_release>2013-09-25</map_release>
         <update>2014-04-16</update>
      </key_dates>
      <title>Structure and Host Adhesion Mechanism of Virulent Lactococcal Phage p2</title>
      <authors_list>
         <author>Bebeacua C</author>
         <author>Tremblay D</author>
         <author>Farenc C</author>
         <author>Chapot MP</author>
         <author>Sadovskaya I</author>
         <author>van Heel M</author>
         <author>Veesler D</author>
         <author>Moineau S</author>
         <author>Cambillau C</author>
      </authors_list>
      <keywords>Lactococcus lactis, Siphoviridae, 936 phages, Bacteriophage, electron microscopy, single-particle, p2</keywords>
   </admin>
   <crossreferences>
      <citation_list>
         <primary_citation>
            <journal_citation published="true">
               <author order="1">Bebeacua C</author>
               <author order="2">Tremblay D</author>
               <author order="3">Farenc C</author>
               <author order="4">Chapot MP</author>
               <author order="5">Sadovskaya I</author>
               <author order="6">van Heel M</author>
               <author order="7">Veesler D</author>
               <author order="8">Moineau S</author>
               <author order="9">Cambillau C</author>
               <title>Structure, adsorption to host, and infection mechanism of virulent lactococcal phage p2.</title>
               <journal>J.VIROL.</journal>
               <volume>87</volume>
               <first_page>12302</first_page>
               <last_page>12312</last_page>
               <year>2013</year>
               <external_references type="PUBMED">24027307</external_references>
               <external_references type="DOI">doi:10.1128/JVI.02033-13</external_references>
            </journal_citation>
         </primary_citation>
      </citation_list>
   </crossreferences>
   <sample>
      <name>Capsid of Lactococcal phage p2</name>
      <supramolecule_list>
         <sample_supramolecule supramolecule_id="1000">
            <name>Capsid of Lactococcal phage p2</name>
            <oligomeric_state>60-mer</oligomeric_state>
            <number_unique_components>1</number_unique_components>
            <molecular_weight>
               <experimental units="MDa">3</experimental>
               <theoretical units="MDa">3</theoretical>
            </molecular_weight>
         </sample_supramolecule>
         <virus_supramolecule supramolecule_id="1">
            <name synonym="Lactococcal phage p2">Lactococcus lactis phage p2</name>
            <details>The capsid was selected from a sample containing entire Lactococcal phages p2.</details>
            <sci_species_name ncbi="100641">Lactococcus lactis phage p2</sci_species_name>
            <natural_host database="NCBI">
               <organism>Lactococcal lactis</organism>
               <strain>NZ9000</strain>
               <synonym_organism>BACTERIA(EUBACTERIA)</synonym_organism>
            </natural_host>
            <host_system database="NCBI">
               </host_system>
            <virus_shell shell_id="1">
               <name>T7</name>
               <diameter units="&#8491;">660</diameter>
               <triangulation>7</triangulation>
            </virus_shell>
            <virus_type>OTHER</virus_type>
            <virus_isolate>SPECIES</virus_isolate>
            <virus_enveloped>false</virus_enveloped>
            <virus_empty>false</virus_empty>
            <syn_species_name>Lactococcal phage p2</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>50 mM Tris-HCl, 100 mM NaCl, 8 mM MgSO4</details>
               </buffer>
               <grid>
                  <details>Quantifoil grids</details>
               </grid>
               <vitrification>
                  <cryogen_name>ETHANE</cryogen_name>
                  <chamber_humidity units="percentage">100</chamber_humidity>
                  <instrument>FEI VITROBOT MARK I</instrument>
                  <method>Blot for 2 seconds before plunging</method>
               </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>FIELD EMISSION GUN</electron_source>
               <acceleration_voltage units="kV">200</acceleration_voltage>
               <nominal_cs units="mm">2.2</nominal_cs>
               <nominal_defocus_min units="&#181;m">0.001</nominal_defocus_min>
               <nominal_defocus_max units="&#181;m">0.002</nominal_defocus_max>
               <nominal_magnification>50000.0</nominal_magnification>
               <specimen_holder_model>GATAN LIQUID NITROGEN</specimen_holder_model>
               <alignment_procedure>
                  <legacy>
                     <astigmatism>Objective lens astigmatism was corrected at 100,000 times magnification.</astigmatism>
                  </legacy>
               </alignment_procedure>
               <date>2009-07-01</date>
               <image_recording_list>
                  <image_recording>
                     <film_or_detector_model category="CCD">GENERIC TVIPS (4k x 4k)</film_or_detector_model>
                     <digitization_details>
                        <sampling_interval units="&#181;m">3.53</sampling_interval>
                     </digitization_details>
                     <number_real_images>200</number_real_images>
                     <average_electron_dose_per_image units="e/&#8491;^2">10</average_electron_dose_per_image>
                  </image_recording>
               </image_recording_list>
            </single_particle_microscopy>
         </microscopy_list>
         <singleparticle_processing image_processing_id="1">
            <details>Reconstruction imposing Icosahedral reconstruction</details>
            <ctf_correction>
               <details>Images</details>
            </ctf_correction>
            <final_reconstruction>
               <applied_symmetry>
                  <point_group>I</point_group>
               </applied_symmetry>
               <algorithm>OTHER</algorithm>
               <resolution res_type="BY AUTHOR" units="&#8491;">13.0</resolution>
               <resolution_method>OTHER</resolution_method>
               <software_list>
                  <software>
                     <name>IMAGIC</name>
                  </software>
               </software_list>
               <number_images_used>3329</number_images_used>
            </final_reconstruction>
         </singleparticle_processing>
      </structure_determination>
   </structure_determination_list>
   <map format="CCP4" size_kbytes="31251">
      <file>emd_2462.map.gz</file>
      <symmetry>
         <space_group>1</space_group>
      </symmetry>
      <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
      <dimensions>
         <col>200</col>
         <row>200</row>
         <sec>200</sec>
      </dimensions>
      <origin>
         <col>-100</col>
         <row>-100</row>
         <sec>-100</sec>
      </origin>
      <spacing>
         <x>200</x>
         <y>200</y>
         <z>200</z>
      </spacing>
      <cell>
         <a units="&#8491;">706.0</a>
         <b units="&#8491;">706.0</b>
         <c units="&#8491;">706.0</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>-4.54166365</minimum>
         <maximum>7.45390415</maximum>
         <average>0.08800913</average>
         <std>0.73049051</std>
      </statistics>
      <pixel_spacing>
         <x units="&#8491;">3.53</x>
         <y units="&#8491;">3.53</y>
         <z units="&#8491;">3.53</z>
      </pixel_spacing>
      <contour_list>
         <contour primary="true">
            <level>0.5</level>
            <source>AUTHOR</source>
         </contour>
      </contour_list>
      <annotation_details>Icosahedral reconstruction of the capsid of lactococcal phage p2.</annotation_details>
      <details>::::EMDATABANK.org::::EMD-2462::::</details>
   </map>
   <interpretation>
      <modelling_list>
         <modelling>
            <initial_model>
               <access_code>1OHG</access_code>
            </initial_model>
            <refinement_protocol>RIGID BODY FIT</refinement_protocol>
            <software_list>
               <software>
                  <name>Chimera</name>
               </software>
            </software_list>
            <details>60 copies of the hexamer of HK97 MCP were manually fitted and automatically refined with Chimera</details>
            <refinement_space>REAL</refinement_space>
         </modelling>
      </modelling_list>
      <figure_list>
         <figure>
            <file>emd_2462.png</file>
         </figure>
      </figure_list>
   </interpretation>
</emd>