<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" emdb_id="EMD-3418" 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>2016-04-29</deposition>
         <header_release>2016-05-18</header_release>
         <map_release>2016-06-08</map_release>
         <update>2017-07-26</update>
      </key_dates>
      <title>Subtomogram average of 80S ribosomes obtained using the VPP</title>
      <authors_list>
         <author>Khoshouei M</author>
         <author>Pfeffer S</author>
         <author>Baumeister W</author>
         <author>Foerster F</author>
         <author>Danev R</author>
      </authors_list>
      <keywords>Ribosome, cryo-electron tomography, subtomogram averaging, phase plate</keywords>
   </admin>
   <crossreferences>
      <citation_list>
         <primary_citation>
            <journal_citation published="true">
               <author order="1">Khoshouei M</author>
               <author order="2">Pfeffer S</author>
               <author order="3">Baumeister W</author>
               <author order="4">Foerster F</author>
               <author order="5">Danev R</author>
               <title>Subtomogram analysis using the Volta phase plate</title>
               <journal>J.STRUCT.BIOL.</journal>
               <volume>197</volume>
               <first_page>94</first_page>
               <last_page>101</last_page>
               <year>2017</year>
               <external_references type="PUBMED">27235783</external_references>
               <external_references type="DOI">doi:10.1016/j.jsb.2016.05.009</external_references>
            </journal_citation>
         </primary_citation>
      </citation_list>
   </crossreferences>
   <sample>
      <name>80S ribosome</name>
      <supramolecule_list>
         <sample_supramolecule supramolecule_id="1000">
            <name>80S ribosome</name>
            <number_unique_components>1</number_unique_components>
         </sample_supramolecule>
         <complex_supramolecule supramolecule_id="1">
            <name>80S ribosome</name>
            <recombinant_exp_flag>false</recombinant_exp_flag>
            <natural_source database="NCBI">
               <organism ncbi="9986">Oryctolagus cuniculus</organism>
               <synonym_organism>Rabbit</synonym_organism>
               <cell>Reticulocyte</cell>
               <cellular_location>Cytoplasm</cellular_location>
            </natural_source>
            <recombinant_expression database="NCBI">
               </recombinant_expression>
            <ribosome-details>ribosome-eukaryote: ALL</ribosome-details>
         </complex_supramolecule>
      </supramolecule_list>
   </sample>
   <structure_determination_list>
      <structure_determination structure_determination_id="1">
         <method>subtomogramAveraging</method>
         <aggregation_state>particle</aggregation_state>
         <specimen_preparation_list>
            <subtomogram_averaging_preparation preparation_id="1">
               <buffer>
                  <ph>7.6</ph>
                  <details>20mM Hepes, 50mM KCl; 2mM MgCl2</details>
               </buffer>
               <grid>
                  <details>Quantifoil R 2/1</details>
               </grid>
               <vitrification>
                  <cryogen_name>ETHANE-PROPANE MIXTURE</cryogen_name>
                  <instrument>FEI VITROBOT MARK IV</instrument>
                  <method>Blotting time of 3 seconds and a blot force of 0 before plunging</method>
               </vitrification>
            </subtomogram_averaging_preparation>
         </specimen_preparation_list>
         <microscopy_list>
            <subtomogram_averaging_microscopy microscopy_id="1">
               <microscope>FEI TITAN</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_defocus_min units="&#181;m">0.0</nominal_defocus_min>
               <nominal_defocus_max units="&#181;m">0.0</nominal_defocus_max>
               <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
               <specialist_optics>
                  <energy_filter>
                     <name>GIF Quantum</name>
                     <lower_energy_threshold units="eV">0.0</lower_energy_threshold>
                     <upper_energy_threshold units="eV">20.0</upper_energy_threshold>
                  </energy_filter>
               </specialist_optics>
               <date>2015-05-06</date>
               <image_recording_list>
                  <image_recording>
                     <film_or_detector_model category="CCD">GATAN K2 SUMMIT (4k x 4k)</film_or_detector_model>
                     <number_real_images>80</number_real_images>
                     <average_electron_dose_per_image units="e/&#8491;^2">30</average_electron_dose_per_image>
                  </image_recording>
               </image_recording_list>
               <tilt_series>
                  <axis1>
                     <min_angle units="deg">-20</min_angle>
                     <max_angle units="deg">20</max_angle>
                  </axis1>
               </tilt_series>
            </subtomogram_averaging_microscopy>
         </microscopy_list>
         <subtomogram_averaging_processing image_processing_id="1">
            <final_reconstruction>
               <applied_symmetry>
                  <point_group>C1</point_group>
               </applied_symmetry>
               <resolution res_type="BY AUTHOR" units="&#8491;">9.6</resolution>
               <resolution_method>OTHER</resolution_method>
               <software_list>
                  <software>
                     <name>TOM, AV3, PyTom</name>
                  </software>
               </software_list>
               <number_subtomograms_used>1400</number_subtomograms_used>
            </final_reconstruction>
            <ctf_correction>
               <details>each tilt image</details>
            </ctf_correction>
         </subtomogram_averaging_processing>
      </structure_determination>
   </structure_determination_list>
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      <file>emd_3418.map.gz</file>
      <symmetry>
         <space_group>1</space_group>
      </symmetry>
      <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
      <dimensions>
         <col>160</col>
         <row>160</row>
         <sec>160</sec>
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         <col>0</col>
         <row>0</row>
         <sec>0</sec>
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      <spacing>
         <x>160</x>
         <y>160</y>
         <z>160</z>
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      <cell>
         <a units="&#8491;">419.19998</a>
         <b units="&#8491;">419.19998</b>
         <c units="&#8491;">419.19998</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>-6.65906477</minimum>
         <maximum>12.266580579999999</maximum>
         <average>-0.00000001</average>
         <std>0.99999988</std>
      </statistics>
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      <contour_list>
         <contour primary="true">
            <level>3.24</level>
            <source>AUTHOR</source>
         </contour>
      </contour_list>
      <annotation_details>Subtomogram average of the 80S ribosome obtained with the VPP</annotation_details>
      <details>::::EMDATABANK.org::::EMD-3418::::</details>
   </map>
   <interpretation>
      <figure_list>
         <figure>
            <file>emd_3418.jpg</file>
         </figure>
      </figure_list>
   </interpretation>
</emd>