<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" emdb_id="EMD-2667" 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>2014-06-04</deposition>
         <header_release>2014-07-02</header_release>
         <map_release>2015-06-17</map_release>
         <update>2015-06-17</update>
      </key_dates>
      <title>Intact Shigella Type III secretion injectisome</title>
      <authors_list>
         <author>Hu B</author>
         <author>Margolin W</author>
         <author>Rohde J</author>
         <author>Picking WL</author>
         <author>Picking WD</author>
         <author>Liu J</author>
      </authors_list>
      <keywords>Secretion machine, T3SS, cytoplasmic complex, injectisome</keywords>
   </admin>
   <crossreferences>
      <citation_list>
         <primary_citation>
            <journal_citation published="true">
               <author order="1">Hu B</author>
               <author order="2">Morado DR</author>
               <author order="3">Margolin W</author>
               <author order="4">Rohde JR</author>
               <author order="5">Arizmendi O</author>
               <author order="6">Picking WL</author>
               <author order="7">Picking WD</author>
               <author order="8">Liu J</author>
               <title>Visualization of the type III secretion sorting platform of Shigella flexneri</title>
               <journal>PROC.NAT.ACAD.SCI.USA</journal>
               <volume>112</volume>
               <first_page>1047</first_page>
               <last_page>1052</last_page>
               <year>2015</year>
               <external_references type="PUBMED">25583506</external_references>
               <external_references type="DOI">doi:10.1073/pnas.1411610112</external_references>
            </journal_citation>
         </primary_citation>
      </citation_list>
   </crossreferences>
   <sample>
      <name>Shigella flexneri serotype 5a injectisome</name>
      <supramolecule_list>
         <sample_supramolecule supramolecule_id="1000">
            <name>Shigella flexneri serotype 5a injectisome</name>
            <number_unique_components>1</number_unique_components>
         </sample_supramolecule>
         <organelle_or_cellular_component_supramolecule supramolecule_id="1">
            <name>Shigella flexneri serotype 5a injectisome</name>
            <details>Minicell derived from Shigella flexneri serotype 5a</details>
            <number_of_copies>25</number_of_copies>
            <recombinant_exp_flag>false</recombinant_exp_flag>
            <natural_source database="NCBI">
               <organism ncbi="424718">Shigella flexneri 5a</organism>
               <strain>Shigella flexneri serotype 5a</strain>
            </natural_source>
            <recombinant_expression database="NCBI">
               </recombinant_expression>
         </organelle_or_cellular_component_supramolecule>
      </supramolecule_list>
   </sample>
   <structure_determination_list>
      <structure_determination structure_determination_id="1">
         <method>subtomogramAveraging</method>
         <aggregation_state>cell</aggregation_state>
         <specimen_preparation_list>
            <subtomogram_averaging_preparation preparation_id="1">
               <buffer>
                  <ph>7.0</ph>
               </buffer>
               <grid>
                  <details>200 mesh holey carbon grids</details>
               </grid>
               <vitrification>
                  <cryogen_name>ETHANE</cryogen_name>
                  <chamber_humidity units="percentage">80</chamber_humidity>
                  <chamber_temperature units="K">120</chamber_temperature>
                  <instrument>OTHER</instrument>
                  <method>Blot for 3 seconds before plunging</method>
               </vitrification>
            </subtomogram_averaging_preparation>
         </specimen_preparation_list>
         <microscopy_list>
            <subtomogram_averaging_microscopy microscopy_id="1">
               <microscope>FEI POLARA 300</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</nominal_cs>
               <nominal_defocus_min units="&#181;m">5.0</nominal_defocus_min>
               <nominal_defocus_max units="&#181;m">8.0</nominal_defocus_max>
               <nominal_magnification>15500.0</nominal_magnification>
               <specimen_holder_model>SIDE ENTRY, EUCENTRIC</specimen_holder_model>
               <alignment_procedure>
                  <legacy>
                     <astigmatism>Objective lens astigmatism was corrected at 100,000 times magnification</astigmatism>
                  </legacy>
               </alignment_procedure>
               <details>Tilt series were collected in 2x2 binning.</details>
               <date>2014-01-01</date>
               <image_recording_list>
                  <image_recording>
                     <film_or_detector_model category="CCD">GATAN K2 (4k x 4k)</film_or_detector_model>
                     <digitization_details>
                        <sampling_interval units="&#181;m">5</sampling_interval>
                     </digitization_details>
                     <number_real_images>28548</number_real_images>
                     <average_electron_dose_per_image units="e/&#8491;^2">60</average_electron_dose_per_image>
                     <bits_per_pixel>16.</bits_per_pixel>
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               </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>The subtomograms were visually selected.</details>
            <final_reconstruction>
               <applied_symmetry>
                  <point_group>C1</point_group>
               </applied_symmetry>
               <algorithm>OTHER</algorithm>
               <resolution res_type="BY AUTHOR" units="&#8491;">34.0</resolution>
               <resolution_method>OTHER</resolution_method>
               <software_list>
                  <software>
                     <name>IMOD, RAPTOR, PROTOMO</name>
                  </software>
               </software_list>
               <number_subtomograms_used>1448</number_subtomograms_used>
            </final_reconstruction>
            <final_three_d_classification>
               <number_classes>8</number_classes>
            </final_three_d_classification>
         </subtomogram_averaging_processing>
      </structure_determination>
   </structure_determination_list>
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      <file>emd_2667.map.gz</file>
      <symmetry>
         <space_group>1</space_group>
      </symmetry>
      <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
      <dimensions>
         <col>120</col>
         <row>120</row>
         <sec>260</sec>
      </dimensions>
      <origin>
         <col>-60</col>
         <row>-60</row>
         <sec>-130</sec>
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         <x>120</x>
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         <b units="&#8491;">600.0</b>
         <c units="&#8491;">1300.0</c>
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         <beta units="deg">90.0</beta>
         <gamma units="deg">90.0</gamma>
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      <axis_order>
         <fast>X</fast>
         <medium>Y</medium>
         <slow>Z</slow>
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      <statistics>
         <minimum>-5.61434698</minimum>
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         <std>0.99999994</std>
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         <y units="&#8491;">5.0</y>
         <z units="&#8491;">5.0</z>
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      <contour_list>
         <contour primary="true">
            <level>0.2</level>
            <source>AUTHOR</source>
         </contour>
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      <annotation_details>Reconstruction of an intact T3SS machine</annotation_details>
      <details>::::EMDATABANK.org::::EMD-2667::::</details>
   </map>
</emd>