<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" emdb_id="EMD-1993" 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>2011-11-18</deposition>
         <header_release>2012-01-06</header_release>
         <map_release>2012-01-06</map_release>
         <update>2012-02-03</update>
      </key_dates>
      <title>Negative stain reconstruction of recombinantly expressed yeast proteasome lid</title>
      <authors_list>
         <author>Lander GC</author>
         <author>Estrin E</author>
         <author>Matyskiela M</author>
         <author>Bashore C</author>
         <author>Nogales E</author>
         <author>Martin A</author>
      </authors_list>
      <keywords>26S, 19S, proteasome, yeast lid, regulatory particle, ubiquitin recognition, deubiquitination, AAA-ATPase</keywords>
   </admin>
   <crossreferences>
      <citation_list>
         <primary_citation>
            <journal_citation published="true">
               <author order="1">Lander GC</author>
               <author order="2">Estrin E</author>
               <author order="3">Matyskiela ME</author>
               <author order="4">Bashore C</author>
               <author order="5">Nogales E</author>
               <author order="6">Martin A</author>
               <title>Complete subunit architecture of the proteasome regulatory particle.</title>
               <journal>NATURE</journal>
               <volume>482</volume>
               <first_page>186</first_page>
               <last_page>191</last_page>
               <year>2012</year>
               <external_references type="PUBMED">22237024</external_references>
               <external_references type="DOI">doi:10.1038/nature10774</external_references>
            </journal_citation>
         </primary_citation>
      </citation_list>
   </crossreferences>
   <sample>
      <name>recombinantly expressed yeast lid</name>
      <supramolecule_list>
         <sample_supramolecule supramolecule_id="1000">
            <name>recombinantly expressed yeast lid</name>
            <details>monodisperse</details>
            <oligomeric_state>8 subunit complex</oligomeric_state>
            <number_unique_components>1</number_unique_components>
            <molecular_weight>
               <experimental units="MDa">0.361</experimental>
               <theoretical units="MDa">0.361</theoretical>
               <method>Mass Spectrometry</method>
            </molecular_weight>
         </sample_supramolecule>
      </supramolecule_list>
      <macromolecule_list>
         <protein_or_peptide macromolecule_id="1">
            <name synonym="lid">lid</name>
            <natural_source database="NCBI">
               <organism ncbi="4932">Saccharomyces cerevisiae</organism>
               <strain>W303</strain>
               <synonym_organism>Baker's Yeast</synonym_organism>
            </natural_source>
            <molecular_weight>
               <experimental units="MDa">0.361</experimental>
               <theoretical units="MDa">0.361</theoretical>
            </molecular_weight>
            <details>all subunits were recombinantly expressed</details>
            <number_of_copies>1</number_of_copies>
            <oligomeric_state>monomer</oligomeric_state>
            <recombinant_exp_flag>true</recombinant_exp_flag>
            <recombinant_expression database="NCBI">
               <recombinant_organism>Escherichia coli BL21-star (DE3)</recombinant_organism>
               <recombinant_plasmid>pAM001,pAM002,pAM003</recombinant_plasmid>
            </recombinant_expression>
            <sequence>
               <external_references type="GO">GO:0008541</external_references>
               <external_references type="INTERPRO">IPR002015</external_references>
            </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">0.009</concentration>
               <buffer>
                  <ph>7.6</ph>
                  <details>25mM HEPES, 100mM NaCl, 100mM KCl, 5% glycerol</details>
               </buffer>
               <staining>
                  <type>NEGATIVE</type>
                  <details>Protein adsorbed to grid for 1 minute, then passed over four 50uL drops of 2% w/v uranyl formate, 5 seconds on each drop</details>
               </staining>
               <grid>
                  <details>200 mesh Cu grid</details>
               </grid>
               <vitrification>
                  <cryogen_name>NONE</cryogen_name>
                  <instrument>OTHER</instrument>
               </vitrification>
            </single_particle_preparation>
         </specimen_preparation_list>
         <microscopy_list>
            <single_particle_microscopy microscopy_id="1">
               <microscope>FEI TECNAI 20</microscope>
               <illumination_mode>FLOOD BEAM</illumination_mode>
               <imaging_mode>BRIGHT FIELD</imaging_mode>
               <electron_source>FIELD EMISSION GUN</electron_source>
               <acceleration_voltage units="kV">120</acceleration_voltage>
               <nominal_cs units="mm">2.2</nominal_cs>
               <nominal_defocus_min units="&#181;m">0.5</nominal_defocus_min>
               <nominal_defocus_max units="&#181;m">1.2</nominal_defocus_max>
               <nominal_magnification>80000.0</nominal_magnification>
               <calibrated_magnification>80000.0</calibrated_magnification>
               <specimen_holder_model>SIDE ENTRY, EUCENTRIC</specimen_holder_model>
               <temperature>
                  <temperature_min units="K">78</temperature_min>
                  <temperature_max units="K">78</temperature_max>
                  <temperature_average units="K">78</temperature_average>
               </temperature>
               <alignment_procedure>
                  <legacy>
                     <astigmatism>objective lens astigmatism was corrected at 210,000 times magnification</astigmatism>
                     <electron_beam_tilt_params>0</electron_beam_tilt_params>
                  </legacy>
               </alignment_procedure>
               <details>Data acquired using Leginon</details>
               <date>2011-08-22</date>
               <image_recording_list>
                  <image_recording>
                     <film_or_detector_model category="CCD">GENERIC GATAN (4k x 4k)</film_or_detector_model>
                     <number_real_images>303</number_real_images>
                     <average_electron_dose_per_image units="e/&#8491;^2">20</average_electron_dose_per_image>
                  </image_recording>
               </image_recording_list>
               <specimen_holder>Room temp single tilt</specimen_holder>
            </single_particle_microscopy>
         </microscopy_list>
         <singleparticle_processing image_processing_id="1">
            <details>Image processing performed in the Appion processing environment. 3D reconstruction performed using EMAN2 and SPARX libraries</details>
            <ctf_correction>
               <details>whole micrograph</details>
            </ctf_correction>
            <final_reconstruction>
               <applied_symmetry>
                  <point_group>C1</point_group>
               </applied_symmetry>
               <algorithm>OTHER</algorithm>
               <resolution res_type="BY AUTHOR" units="&#8491;">16.0</resolution>
               <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
               <software_list>
                  <software>
                     <name>EMAN2 SPARX</name>
                  </software>
               </software_list>
               <number_images_used>29345</number_images_used>
            </final_reconstruction>
         </singleparticle_processing>
      </structure_determination>
   </structure_determination_list>
   <map format="CCP4" size_kbytes="8193">
      <file>emd_1993.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>0</col>
         <row>0</row>
         <sec>0</sec>
      </origin>
      <spacing>
         <x>128</x>
         <y>128</y>
         <z>128</z>
      </spacing>
      <cell>
         <a units="&#8491;">353.28</a>
         <b units="&#8491;">353.28</b>
         <c units="&#8491;">353.28</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>-4.75049</minimum>
         <maximum>20.128599999999999</maximum>
         <average>0.00000000735695</average>
         <std>1.0</std>
      </statistics>
      <pixel_spacing>
         <x units="&#8491;">2.76</x>
         <y units="&#8491;">2.76</y>
         <z units="&#8491;">2.76</z>
      </pixel_spacing>
      <contour_list>
         <contour primary="true">
            <level>4.5</level>
            <source>AUTHOR</source>
         </contour>
      </contour_list>
      <annotation_details>Map of recombinantly expressed Saccharomyces cerevisiae proteasome lid</annotation_details>
      <details>::::EMDATABANK.org::::EMD-1993::::</details>
   </map>
</emd>