<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" emdb_id="EMD-1081" 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>2004-05-13</deposition>
         <header_release>2004-05-14</header_release>
         <map_release>2004-07-14</map_release>
         <update>2011-05-26</update>
      </key_dates>
      <title>Seeing GroEL at 6 A resolution by single particle electron cryomicroscopy.</title>
      <authors_list>
         <author>Ludtke SJ</author>
         <author>Chen D</author>
         <author>Song J</author>
         <author>Chuang DT</author>
         <author>Chiu W</author>
      </authors_list>
      <keywords>
         </keywords>
   </admin>
   <crossreferences>
      <citation_list>
         <primary_citation>
            <journal_citation published="true">
               <author order="1">Ludtke SJ</author>
               <author order="2">Chen DH</author>
               <author order="3">Song JL</author>
               <author order="4">Chuang DT</author>
               <author order="5">Chiu W</author>
               <title>Seeing GroEL at 6 A resolution by single particle electron cryomicroscopy.</title>
               <journal>STRUCTURE</journal>
               <volume>12</volume>
               <first_page>1129</first_page>
               <last_page>1136</last_page>
               <year>2004</year>
               <external_references type="PUBMED">15242589</external_references>
               <external_references type="DOI">doi:10.1016/j.str.2004.05.006</external_references>
            </journal_citation>
         </primary_citation>
      </citation_list>
   </crossreferences>
   <sample>
      <name>native naked GroEL</name>
      <supramolecule_list>
         <sample_supramolecule supramolecule_id="1000">
            <name>native naked GroEL</name>
            <oligomeric_state>homo 14-mer</oligomeric_state>
            <number_unique_components>1</number_unique_components>
            <molecular_weight>
               <theoretical units="MDa">0.8</theoretical>
            </molecular_weight>
         </sample_supramolecule>
      </supramolecule_list>
      <macromolecule_list>
         <protein_or_peptide macromolecule_id="1">
            <name>GroEL</name>
            <natural_source database="NCBI">
               <organism ncbi="562">Escherichia coli</organism>
            </natural_source>
            <molecular_weight>
               <experimental units="MDa">0.057</experimental>
            </molecular_weight>
            <number_of_copies>14</number_of_copies>
            <oligomeric_state>14mer</oligomeric_state>
            <recombinant_exp_flag>true</recombinant_exp_flag>
            <recombinant_expression database="NCBI">
               <recombinant_organism>ESts CG-712</recombinant_organism>
               <recombinant_plasmid>pGroESL</recombinant_plasmid>
            </recombinant_expression>
            <sequence>
               </sequence>
         </protein_or_peptide>
      </macromolecule_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">1.0</concentration>
               <vitrification>
                  <cryogen_name>ETHANE</cryogen_name>
                  <instrument>HOMEMADE PLUNGER</instrument>
                  <details>Vitrification instrument: Manual gravity plunger</details>
               </vitrification>
            </single_particle_preparation>
         </specimen_preparation_list>
         <microscopy_list>
            <single_particle_microscopy microscopy_id="1">
               <microscope>JEOL 2010F</microscope>
               <illumination_mode>FLOOD BEAM</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">1.0</nominal_cs>
               <nominal_defocus_min units="&#181;m">0.794</nominal_defocus_min>
               <nominal_defocus_max units="&#181;m">2.56</nominal_defocus_max>
               <nominal_magnification>50000.0</nominal_magnification>
               <specimen_holder_model>GATAN LIQUID NITROGEN</specimen_holder_model>
               <image_recording_list>
                  <image_recording>
                     <film_or_detector_model category="FILM">KODAK SO-163 FILM</film_or_detector_model>
                     <digitization_details>
                        <scanner>ZEISS SCAI</scanner>
                        <sampling_interval units="&#181;m">7</sampling_interval>
                     </digitization_details>
                     <number_real_images>42</number_real_images>
                     <average_electron_dose_per_image units="e/&#8491;^2">18</average_electron_dose_per_image>
                     <details>Data was median filtered to 10.5 microns/pixel
        after scanning.</details>
                     <bits_per_pixel>8.</bits_per_pixel>
                  </image_recording>
               </image_recording_list>
               <specimen_holder>Side entry</specimen_holder>
            </single_particle_microscopy>
         </microscopy_list>
         <singleparticle_processing image_processing_id="1">
            <details>Note that class averages are EMAN-style
          reference-based,       not MSA.</details>
            <ctf_correction>
               <details>per-particle phase flipping pre-processing,
        amplitude       correction during class averaging</details>
            </ctf_correction>
            <final_reconstruction>
               <applied_symmetry>
                  <point_group>D7</point_group>
               </applied_symmetry>
               <resolution res_type="BY AUTHOR" units="&#8491;">6.0</resolution>
               <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
               <software_list>
                  <software>
                     <name>EMAN</name>
                  </software>
               </software_list>
               <number_images_used>39085</number_images_used>
            </final_reconstruction>
            <final_two_d_classification>
               <number_classes>295</number_classes>
            </final_two_d_classification>
         </singleparticle_processing>
      </structure_determination>
   </structure_determination_list>
   <map format="CCP4" size_kbytes="8193">
      <file>emd_1081.map.gz</file>
      <symmetry>
         <space_group>1</space_group>
      </symmetry>
      <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
      <dimensions>
         <col>128</col>
         <row>128</row>
         <sec>128</sec>
      </dimensions>
      <origin>
         <col>-64</col>
         <row>-64</row>
         <sec>-64</sec>
      </origin>
      <spacing>
         <x>128</x>
         <y>128</y>
         <z>128</z>
      </spacing>
      <cell>
         <a units="&#8491;">264.16</a>
         <b units="&#8491;">264.16</b>
         <c units="&#8491;">264.16</c>
         <alpha units="deg">90</alpha>
         <beta units="deg">90</beta>
         <gamma units="deg">90</gamma>
      </cell>
      <axis_order>
         <fast>X</fast>
         <medium>Y</medium>
         <slow>Z</slow>
      </axis_order>
      <statistics>
         <minimum>-1.19262</minimum>
         <maximum>1.78203</maximum>
         <average>-0.000000000096827</average>
         <std>0.148809</std>
      </statistics>
      <pixel_spacing>
         <x units="&#8491;">2.08</x>
         <y units="&#8491;">2.08</y>
         <z units="&#8491;">2.08</z>
      </pixel_spacing>
      <contour_list>
         <contour primary="true">
            <level>0.209</level>
         </contour>
      </contour_list>
      <annotation_details>This is the density map for the final published
      ~6 A resolution GroEL structure.</annotation_details>
      <details>::::EMDATABANK.org::::EMD-1081::::</details>
   </map>
   <interpretation>
      <modelling_list>
         <modelling>
            <initial_model>
               <access_code>1OEL</access_code>
            </initial_model>
            <refinement_protocol>RIGID BODY FIT</refinement_protocol>
            <software_list>
               <software>
                  <name>foldhunter, EMAN</name>
               </software>
            </software_list>
            <details>Protocol: Rigid Body. rigid body fitting of 1 monomer from 1OEL initially, followed by rigid body refinement of each domain, apical, intermediate and equatorial.</details>
            <target_criteria>correlation coefficient</target_criteria>
            <refinement_space>REAL</refinement_space>
         </modelling>
      </modelling_list>
   </interpretation>
</emd>