<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" emdb_id="EMD-3200" 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>2015-10-19</deposition>
         <header_release>2015-11-04</header_release>
         <map_release>2015-12-16</map_release>
         <update>2016-02-17</update>
      </key_dates>
      <title>Cryo-EM structure of the Rix1dC mutant pre-60S particle</title>
      <authors_list>
         <author>Barrio-Garcia C</author>
         <author>Thoms M</author>
         <author>Flemming D</author>
         <author>Kater L</author>
         <author>Berninghausen O</author>
         <author>Bassler J</author>
         <author>Beckmann R</author>
         <author>Hurt E</author>
      </authors_list>
      <keywords>ribosome, ribosome biogenesis, ribosome assembly, pre-60S, 5S RNP, assembly intermediate, cryo-EM, Rea1, Rix1 complex, Sda1</keywords>
   </admin>
   <crossreferences>
      <citation_list>
         <primary_citation>
            <journal_citation published="true">
               <author order="1">Barrio-Garcia C</author>
               <author order="2">Thoms M</author>
               <author order="3">Flemming D</author>
               <author order="4">Kater L</author>
               <author order="5">Berninghausen O</author>
               <author order="6">Bassler J</author>
               <author order="7">Beckmann R</author>
               <author order="8">Hurt E</author>
               <title>Architecture of the Rix1-Rea1 checkpoint machinery during pre-60S-ribosome remodeling.</title>
               <journal>NAT.STRUCT.MOL.BIOL.</journal>
               <volume>23</volume>
               <first_page>37</first_page>
               <last_page>44</last_page>
               <year>2016</year>
               <external_references type="PUBMED">26619264</external_references>
               <external_references type="DOI">doi:10.1038/nsmb.3132</external_references>
            </journal_citation>
         </primary_citation>
      </citation_list>
   </crossreferences>
   <sample>
      <name>Rix1dC mutant pre60S particle</name>
      <supramolecule_list>
         <sample_supramolecule supramolecule_id="1000">
            <name>Rix1dC mutant pre60S particle</name>
            <number_unique_components>1</number_unique_components>
         </sample_supramolecule>
         <complex_supramolecule supramolecule_id="1">
            <name synonym="pre-60S">pre-60S particle</name>
            <recombinant_exp_flag>false</recombinant_exp_flag>
            <natural_source database="NCBI">
               <organism ncbi="4932">Saccharomyces cerevisiae</organism>
               <synonym_organism>yeast</synonym_organism>
            </natural_source>
            <recombinant_expression database="NCBI">
               </recombinant_expression>
            <ribosome-details>ribosome-eukaryote: LSU 60S</ribosome-details>
         </complex_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">0.8</concentration>
               <buffer>
                  <ph>7.5</ph>
                  <details>50 mM Tris-HCl, 100 mM NaCl, 1.5 mM or 5 mM MgCl2</details>
               </buffer>
               <grid>
                  <details>The freshly prepared pre-60S sample was applied to 2 nm pre-coated Quantifoil holey carbon supported grids and vitrified</details>
               </grid>
               <vitrification>
                  <cryogen_name>ETHANE</cryogen_name>
                  <chamber_humidity units="percentage">95</chamber_humidity>
                  <instrument>FEI VITROBOT MARK IV</instrument>
                  <method>Blot for 3 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>SPOT SCAN</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">1.29</nominal_defocus_min>
               <nominal_defocus_max units="&#181;m">3.39</nominal_defocus_max>
               <nominal_magnification>75000.0</nominal_magnification>
               <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
               <date>2014-08-29</date>
               <image_recording_list>
                  <image_recording>
                     <film_or_detector_model category="CCD">TVIPS TEMCAM-F816 (8k x 8k)</film_or_detector_model>
                     <number_real_images>2659</number_real_images>
                     <average_electron_dose_per_image units="e/&#8491;^2">20</average_electron_dose_per_image>
                  </image_recording>
               </image_recording_list>
            </single_particle_microscopy>
         </microscopy_list>
         <singleparticle_processing image_processing_id="1">
            <details>The particles were selected using the automatic selection program SIGNATURE</details>
            <ctf_correction>
               <details>Subvolumes</details>
            </ctf_correction>
            <final_reconstruction>
               <applied_symmetry>
                  <point_group>C1</point_group>
               </applied_symmetry>
               <algorithm>OTHER</algorithm>
               <resolution res_type="BY AUTHOR" units="&#8491;">11.2</resolution>
               <resolution_method>OTHER</resolution_method>
               <software_list>
                  <software>
                     <name>Signature, Spider</name>
                  </software>
               </software_list>
               <number_images_used>26082</number_images_used>
            </final_reconstruction>
         </singleparticle_processing>
      </structure_determination>
   </structure_determination_list>
   <map format="CCP4" size_kbytes="465218">
      <file>emd_3200.map.gz</file>
      <symmetry>
         <space_group>1</space_group>
      </symmetry>
      <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
      <dimensions>
         <col>492</col>
         <row>492</row>
         <sec>492</sec>
      </dimensions>
      <origin>
         <col>0</col>
         <row>0</row>
         <sec>0</sec>
      </origin>
      <spacing>
         <x>492</x>
         <y>492</y>
         <z>492</z>
      </spacing>
      <cell>
         <a units="&#8491;">508.974</a>
         <b units="&#8491;">508.974</b>
         <c units="&#8491;">508.974</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>-0.13435788</minimum>
         <maximum>0.28068089</maximum>
         <average>0.00148432</average>
         <std>0.01677013</std>
      </statistics>
      <pixel_spacing>
         <x units="&#8491;">1.0345</x>
         <y units="&#8491;">1.0345</y>
         <z units="&#8491;">1.0345</z>
      </pixel_spacing>
      <contour_list>
         <contour primary="true">
            <level>0.018</level>
            <source>AUTHOR</source>
         </contour>
      </contour_list>
      <annotation_details>Reconstructed Rix1 mutant pre-60S particle</annotation_details>
      <details>::::EMDATABANK.org::::EMD-3200::::</details>
   </map>
</emd>