<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" emdb_id="EMD-2762" 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>2014-08-26</deposition>
         <header_release>2014-09-10</header_release>
         <map_release>2014-10-15</map_release>
         <update>2014-11-19</update>
      </key_dates>
      <title>Electron cryo-microscopy of human mitochondrial large ribosomal subunit</title>
      <authors_list>
         <author>Brown A</author>
         <author>Amunts A</author>
         <author>Bai XC</author>
         <author>Sugimoto Y</author>
         <author>Edwards PC</author>
         <author>Murshudov G</author>
         <author>Scheres SHW</author>
         <author>Ramakrishnan V</author>
      </authors_list>
      <keywords>ribosome, translation</keywords>
   </admin>
   <crossreferences>
      <citation_list>
         <primary_citation>
            <journal_citation published="true">
               <author order="1">Brown A</author>
               <author order="2">Amunts A</author>
               <author order="3">Bai XC</author>
               <author order="4">Sugimoto Y</author>
               <author order="5">Edwards PC</author>
               <author order="6">Murshudov G</author>
               <author order="7">Scheres SHW</author>
               <author order="8">Ramakrishnan V</author>
               <title>Structure of the large ribosomal subunit from human mitochondria</title>
               <journal>SCIENCE</journal>
               <volume>346</volume>
               <first_page>718</first_page>
               <last_page>722</last_page>
               <year>2014</year>
               <external_references type="PUBMED">25278503</external_references>
               <external_references type="DOI">doi:10.1126/science.1258026</external_references>
            </journal_citation>
         </primary_citation>
      </citation_list>
      <pdb_list>
         <pdb_reference>
            <pdb_id>3j7y</pdb_id>
            <relationship>
               <in_frame>FULLOVERLAP</in_frame>
            </relationship>
         </pdb_reference>
      </pdb_list>
   </crossreferences>
   <sample>
      <name>Human mitochondrial ribosome</name>
      <supramolecule_list>
         <sample_supramolecule supramolecule_id="1000">
            <name>Human mitochondrial ribosome</name>
            <oligomeric_state>Multimer</oligomeric_state>
            <number_unique_components>1</number_unique_components>
            <molecular_weight>
               <theoretical units="MDa">1.7</theoretical>
            </molecular_weight>
         </sample_supramolecule>
         <organelle_or_cellular_component_supramolecule supramolecule_id="1">
            <name synonym="39S">Large subunit of the human mitochondrial ribosome</name>
            <number_of_copies>1</number_of_copies>
            <oligomeric_state>Monomer</oligomeric_state>
            <recombinant_exp_flag>false</recombinant_exp_flag>
            <natural_source database="NCBI">
               <organism ncbi="9606">Homo sapiens</organism>
               <synonym_organism>Human</synonym_organism>
               <tissue>Kidney</tissue>
               <cell>HEK293</cell>
               <organelle>Mitochondria</organelle>
               <cellular_location>Inner mitochondrial membrane</cellular_location>
            </natural_source>
            <molecular_weight>
               <theoretical units="MDa">1.7</theoretical>
            </molecular_weight>
            <recombinant_expression database="NCBI">
               </recombinant_expression>
         </organelle_or_cellular_component_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">
               <concentration units="mg/mL">0.23</concentration>
               <buffer>
                  <ph>7.45</ph>
                  <details>20 mM Hepes-KOH pH 7.45, 100 mM KCl, 20 mM MgOAc, 2 mM DTT</details>
               </buffer>
               <grid>
                  <details>30 s on glow-discharged holey carbon grids (Quantifoil R2/2), onto which a home-made continuous carbon film</details>
               </grid>
               <vitrification>
                  <cryogen_name>ETHANE</cryogen_name>
                  <chamber_humidity units="percentage">100</chamber_humidity>
                  <chamber_temperature units="K">90</chamber_temperature>
                  <instrument>FEI VITROBOT MARK II</instrument>
                  <method>Blot 2.5 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_defocus_min units="&#181;m">1.5</nominal_defocus_min>
               <nominal_defocus_max units="&#181;m">3.5</nominal_defocus_max>
               <nominal_magnification>59000.0</nominal_magnification>
               <calibrated_magnification>104478.0</calibrated_magnification>
               <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
               <temperature>
                  <temperature_min units="K">80</temperature_min>
                  <temperature_max units="K">90</temperature_max>
                  <temperature_average units="K">85</temperature_average>
               </temperature>
               <alignment_procedure>
                  <legacy>
                     <astigmatism>Objective lens astigmatism was corrected at 59,000 times magnification</astigmatism>
                  </legacy>
               </alignment_procedure>
               <date>2014-04-12</date>
               <image_recording_list>
                  <image_recording>
                     <film_or_detector_model category="CCD">FEI FALCON II (4k x 4k)</film_or_detector_model>
                     <number_real_images>1521</number_real_images>
                     <average_electron_dose_per_image units="e/&#8491;^2">25</average_electron_dose_per_image>
                  </image_recording>
               </image_recording_list>
            </single_particle_microscopy>
         </microscopy_list>
         <singleparticle_processing image_processing_id="1">
            <details>Data were processed to compensate for beam-induced movement.</details>
            <ctf_correction>
               <details>Each particle</details>
            </ctf_correction>
            <final_reconstruction>
               <applied_symmetry>
                  <point_group>C1</point_group>
               </applied_symmetry>
               <resolution res_type="BY AUTHOR" units="&#8491;">3.4</resolution>
               <resolution_method>OTHER</resolution_method>
               <software_list>
                  <software>
                     <name>CTFFIND3, RELION</name>
                  </software>
               </software_list>
               <details>Final resolution was calculated using a soft mask over the large subunit</details>
               <number_images_used>107679</number_images_used>
            </final_reconstruction>
         </singleparticle_processing>
      </structure_determination>
   </structure_determination_list>
   <map format="CCP4" size_kbytes="128001">
      <file>emd_2762.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;">428.80002</a>
         <b units="&#8491;">428.80002</b>
         <c units="&#8491;">428.80002</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>-0.77907181</minimum>
         <maximum>0.96767843</maximum>
         <average>0.00110084</average>
         <std>0.02797702</std>
      </statistics>
      <pixel_spacing>
         <x units="&#8491;">1.34</x>
         <y units="&#8491;">1.34</y>
         <z units="&#8491;">1.34</z>
      </pixel_spacing>
      <contour_list>
         <contour primary="true">
            <level>0.0175</level>
            <source>AUTHOR</source>
         </contour>
      </contour_list>
      <annotation_details>Reconstruction of the large subunit of the human mitochondrial ribosome</annotation_details>
      <details>::::EMDATABANK.org::::EMD-2762::::</details>
   </map>
   <interpretation>
      <segmentation_list>
         <segmentation>
            <file>emd_2762_msk_1.map</file>
            <mask_details format="CCP4" size_kbytes="128001">
               <file>emd_2762_msk_1.map</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;">428.80002</a>
                  <b units="&#8491;">428.80002</b>
                  <c units="&#8491;">428.80002</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>0.0</minimum>
                  <maximum>1.0</maximum>
                  <average>0.05756244</average>
                  <std>0.22739822</std>
               </statistics>
               <pixel_spacing>
                  <x units="&#8491;">1.34</x>
                  <y units="&#8491;">1.34</y>
                  <z units="&#8491;">1.34</z>
               </pixel_spacing>
               <annotation_details>This mask represents the large subunit of the human mitochondrial ribosome</annotation_details>
               <details>::::EMDATABANK.org::::</details>
            </mask_details>
         </segmentation>
      </segmentation_list>
   </interpretation>
   <validation>
      <fsc_curve>
         <file>emd_2762_fsc.xml</file>
      </fsc_curve>
   </validation>
</emd>
