<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" emdb_id="EMD-2982" 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>2015-04-22</deposition>
         <header_release>2015-04-29</header_release>
         <map_release>2015-04-29</map_release>
         <update>2016-02-17</update>
      </key_dates>
      <title>Sub-tomogram average of a mammalian F-type ATP synthase monomer</title>
      <authors_list>
         <author>Jiko C</author>
         <author>Davies KM</author>
         <author>Shinzawa-Itoh K</author>
         <author>Tani K</author>
         <author>Maeda S</author>
         <author>Mills DJ</author>
         <author>Tsukihara T</author>
         <author>Fujiyoshi Y</author>
         <author>Kuehlbrandt W</author>
         <author>Gerle C</author>
      </authors_list>
      <keywords>F-type ATP synthase, Mitochondria Bovine heart</keywords>
   </admin>
   <crossreferences>
      <citation_list>
         <primary_citation>
            <journal_citation published="true">
               <author order="1">Jiko C</author>
               <author order="2">Davies KM</author>
               <author order="3">Shinzawa-Itoh K</author>
               <author order="4">Tani K</author>
               <author order="5">Maeda S</author>
               <author order="6">Mills DJ</author>
               <author order="7">Tsukihara T</author>
               <author order="8">Fujiyoshi Y</author>
               <author order="9">Kuehlbrandt W</author>
               <author order="10">Gerle C</author>
               <title>Bovine F1Fo ATP synthase monomers bend the lipid bilayer in 2D membrane crystals.</title>
               <journal>ELIFE</journal>
               <volume>4</volume>
               <first_page>e06119</first_page>
               <last_page>e06119</last_page>
               <year>2015</year>
               <external_references type="PUBMED">25815585</external_references>
               <external_references type="DOI">doi:10.7554/eLife.06119</external_references>
            </journal_citation>
         </primary_citation>
      </citation_list>
   </crossreferences>
   <sample>
      <name>2D crystal of bovine F-type ATP synthase monomers</name>
      <supramolecule_list>
         <sample_supramolecule supramolecule_id="1000">
            <name>2D crystal of bovine F-type ATP synthase monomers</name>
            <details>2D Membrane crystals
lipids for reconstitution: 1,2-dimyristoyl-sn-glycero-3-phosphocholine</details>
            <oligomeric_state>1</oligomeric_state>
            <number_unique_components>1</number_unique_components>
            <molecular_weight>
               <theoretical units="MDa">0.6</theoretical>
            </molecular_weight>
         </sample_supramolecule>
      </supramolecule_list>
      <macromolecule_list>
         <protein_or_peptide macromolecule_id="1">
            <name>F-type ATP synthase</name>
            <natural_source database="NCBI">
               <organism ncbi="9913">Bos taurus</organism>
               <synonym_organism>cattle</synonym_organism>
               <tissue>Heart</tissue>
               <organelle>Mitochondria</organelle>
               <cellular_location>Mitochondria</cellular_location>
            </natural_source>
            <molecular_weight>
               <theoretical units="MDa">0.6</theoretical>
            </molecular_weight>
            <number_of_copies>1</number_of_copies>
            <oligomeric_state>monomer</oligomeric_state>
            <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>subtomogramAveraging</method>
         <aggregation_state>twoDArray</aggregation_state>
         <specimen_preparation_list>
            <subtomogram_averaging_preparation preparation_id="1">
               <concentration units="mg/mL">10</concentration>
               <buffer>
                  <ph>8.199999999999999</ph>
                  <details>40mM Tris-HCL pH8.2
100mM NaCl
0.02%(w/v)NaN3,
0.5mM ADP,
5mM MgCl2,
0.1mM DTT,
0.1mM EDTA</details>
               </buffer>
               <staining>
                  <type>NEGATIVE</type>
                  <details>Plunge frozen in liquid ethane using home-made freezing device</details>
               </staining>
               <grid>
                  <details>Glow discharged R2/2, 300 copper mesh quantifoil grids</details>
               </grid>
               <vitrification>
                  <cryogen_name>ETHANE</cryogen_name>
                  <chamber_temperature units="K">100</chamber_temperature>
                  <instrument>HOMEMADE PLUNGER</instrument>
                  <method>2D crystals were mixed 1:1 (v/v) with 6nm collodial gold particles. Three microliters of protein/gold sample was applied to R2/2 300 copper mesh quantifoil grids. Access liquid was removed by blotting for 3s with Whatman #4 paper before plunge-freezing in liquid ethane</method>
               </vitrification>
               <details>10mg/ml ATP synthase were mixed with 1,2-dimyristoyl-sn-glycero-3-phosphocholine (Avanti Polar Lipids) using a lipid to protein ratio of 0.2. Detergent was removed by dialysis using 20 microliter Hampton dialysis buttons and 15kDa membrane cuttoff.</details>
            </subtomogram_averaging_preparation>
         </specimen_preparation_list>
         <microscopy_list>
            <subtomogram_averaging_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">2.0</nominal_defocus_min>
               <nominal_defocus_max units="&#181;m">3.0</nominal_defocus_max>
               <nominal_magnification>42000.0</nominal_magnification>
               <calibrated_magnification>14942.0</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">100</temperature_max>
                  <temperature_average units="K">90</temperature_average>
               </temperature>
               <alignment_procedure>
                  <legacy>
                     <astigmatism>Objection lend astigmation was corrected on K2 at magnification used for imaging.</astigmatism>
                  </legacy>
               </alignment_procedure>
               <specialist_optics>
                  <energy_filter>
                     <name>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>
               <details>tomographic tilt series</details>
               <date>2013-02-01</date>
               <image_recording_list>
                  <image_recording>
                     <film_or_detector_model category="CCD">GATAN K2 (4k x 4k)</film_or_detector_model>
                     <number_real_images>80</number_real_images>
                     <average_electron_dose_per_image units="e/&#8491;^2">60</average_electron_dose_per_image>
                  </image_recording>
               </image_recording_list>
               <specimen_holder>Nitrogen cooled</specimen_holder>
               <tilt_series>
                  <axis1>
                     <min_angle units="deg">-60</min_angle>
                     <max_angle units="deg">60</max_angle>
                  </axis1>
               </tilt_series>
            </subtomogram_averaging_microscopy>
         </microscopy_list>
         <subtomogram_averaging_processing image_processing_id="1">
            <details>Subtomograms were selected manually and averaged using PEET (Particle Estimation for Electron Tomography, Boulder)</details>
            <final_reconstruction>
               <applied_symmetry>
                  <point_group>C1</point_group>
               </applied_symmetry>
               <resolution res_type="BY AUTHOR" units="&#8491;">24.0</resolution>
               <resolution_method>OTHER</resolution_method>
               <software_list>
                  <software>
                     <name>IMOD</name>
                  </software>
               </software_list>
               <number_subtomograms_used>2100</number_subtomograms_used>
            </final_reconstruction>
            <ctf_correction>
               <details>IMOD</details>
            </ctf_correction>
            <crystal_parameters>
               <unit_cell>
                  <a units="&#8491;">179.1</a>
                  <b units="&#8491;">171.4</b>
                  <gamma units="deg">94.9</gamma>
               </unit_cell>
               <plane_group>P 1</plane_group>
            </crystal_parameters>
         </subtomogram_averaging_processing>
      </structure_determination>
   </structure_determination_list>
   <map format="CCP4" size_kbytes="440">
      <file>emd_2982.map.gz</file>
      <symmetry>
         <space_group>1</space_group>
      </symmetry>
      <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
      <dimensions>
         <col>40</col>
         <row>39</row>
         <sec>72</sec>
      </dimensions>
      <origin>
         <col>0</col>
         <row>0</row>
         <sec>0</sec>
      </origin>
      <spacing>
         <x>39</x>
         <y>40</y>
         <z>72</z>
      </spacing>
      <cell>
         <a units="&#8491;">132.0</a>
         <b units="&#8491;">128.7</b>
         <c units="&#8491;">237.59999</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>127.086883540000002</minimum>
         <maximum>156.748321529999998</maximum>
         <average>138.239059450000013</average>
         <std>3.54048061</std>
      </statistics>
      <pixel_spacing>
         <x units="&#8491;">3.3</x>
         <y units="&#8491;">3.3</y>
         <z units="&#8491;">3.3</z>
      </pixel_spacing>
      <contour_list>
         <contour primary="true">
            <level>141.800000000000011</level>
            <source>AUTHOR</source>
         </contour>
      </contour_list>
      <annotation_details>Sub-tomogram average of bovine F-type ATP synthase in a 2D crystal</annotation_details>
      <details>::::EMDATABANK.org::::EMD-2982::::</details>
   </map>
</emd>