<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" emdb_id="EMD-2966" 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>2015-03-29</deposition>
         <header_release>2015-05-06</header_release>
         <map_release>2015-07-01</map_release>
         <update>2015-07-01</update>
      </key_dates>
      <title>EM structure of the yeast spliceosomal U4/U6.U5 tri-snRNP</title>
      <authors_list>
         <author>Nguyen THD</author>
         <author>Galej WP</author>
         <author>Bai X-C</author>
         <author>Savva CG</author>
         <author>Newman AJ</author>
         <author>Scheres SHW</author>
         <author>Nagai K</author>
      </authors_list>
      <keywords>Spliceosome, tri-snRNP</keywords>
   </admin>
   <crossreferences>
      <citation_list>
         <primary_citation>
            <journal_citation published="true">
               <author order="1">Nguyen THD</author>
               <author order="2">Galej WP</author>
               <author order="3">Bai X-C</author>
               <author order="4">Savva CG</author>
               <author order="5">Newman AJ</author>
               <author order="6">Scheres SHW</author>
               <author order="7">Nagai K</author>
               <title>The architecture of the spliceosomal U4/U6.U5 tri-snRNP</title>
               <journal>NATURE</journal>
               <volume>523</volume>
               <first_page>47</first_page>
               <last_page>52</last_page>
               <year>2015</year>
               <external_references type="PUBMED">26106855</external_references>
               <external_references type="DOI">doi:10.1038/nature14548</external_references>
            </journal_citation>
         </primary_citation>
      </citation_list>
   </crossreferences>
   <sample>
      <name>Yeast U4/U6.U5 tri-snRNP</name>
      <supramolecule_list>
         <sample_supramolecule supramolecule_id="1000">
            <name>Yeast U4/U6.U5 tri-snRNP</name>
            <number_unique_components>4</number_unique_components>
            <molecular_weight>
               <theoretical units="MDa">1.5</theoretical>
            </molecular_weight>
         </sample_supramolecule>
      </supramolecule_list>
      <macromolecule_list>
         <rna macromolecule_id="1">
            <name>U4 snRNA</name>
            <natural_source database="NCBI">
               <organism ncbi="4932">Saccharomyces cerevisiae</organism>
               <synonym_organism>budding yeast</synonym_organism>
            </natural_source>
            <classification>OTHER</classification>
            <structure>OTHER</structure>
            <synthetic_flag>false</synthetic_flag>
         </rna>
         <rna macromolecule_id="2">
            <name>U5 snRNA</name>
            <natural_source database="NCBI">
               <organism ncbi="4932">Saccharomyces cerevisiae</organism>
               <synonym_organism>budding yeast</synonym_organism>
            </natural_source>
            <classification>OTHER</classification>
            <structure>OTHER</structure>
            <synthetic_flag>false</synthetic_flag>
         </rna>
         <rna macromolecule_id="3">
            <name>U6 snRNA</name>
            <natural_source database="NCBI">
               <organism ncbi="4932">Saccharomyces cerevisiae</organism>
               <synonym_organism>budding yeast</synonym_organism>
            </natural_source>
            <classification>OTHER</classification>
            <structure>OTHER</structure>
            <synthetic_flag>false</synthetic_flag>
         </rna>
         <protein_or_peptide macromolecule_id="4">
            <name>U4/U6.U5 tri-snRNP</name>
            <natural_source database="NCBI">
               <organism ncbi="4932">Saccharomyces cerevisiae</organism>
               <synonym_organism>Budding yeast</synonym_organism>
               <organelle>Nucleus</organelle>
            </natural_source>
            <number_of_copies>1</number_of_copies>
            <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>singleParticle</method>
         <aggregation_state>particle</aggregation_state>
         <specimen_preparation_list>
            <single_particle_preparation preparation_id="1">
               <buffer>
                  <ph>7.9</ph>
               </buffer>
               <grid>
                  <details>400 mesh copper grid with thin carbon support, glow discharged in amylamine atmosphere</details>
               </grid>
               <vitrification>
                  <cryogen_name>ETHANE</cryogen_name>
                  <chamber_humidity units="percentage">100</chamber_humidity>
                  <chamber_temperature units="K">85</chamber_temperature>
                  <instrument>FEI VITROBOT MARK II</instrument>
                  <method>Blot for 2 s before plunging</method>
               </vitrification>
            </single_particle_preparation>
         </specimen_preparation_list>
         <microscopy_list>
            <single_particle_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_magnification>59000.0</nominal_magnification>
               <calibrated_magnification>79096.0</calibrated_magnification>
               <specimen_holder_model>GATAN LIQUID NITROGEN</specimen_holder_model>
               <temperature>
                  <temperature_min units="K">80</temperature_min>
                  <temperature_max units="K">90</temperature_max>
                  <temperature_average units="K">85</temperature_average>
               </temperature>
               <date>2014-06-10</date>
               <image_recording_list>
                  <image_recording>
                     <film_or_detector_model category="CCD">FEI FALCON II (4k x 4k)</film_or_detector_model>
                     <number_real_images>2035</number_real_images>
                     <average_electron_dose_per_image units="e/&#8491;^2">40</average_electron_dose_per_image>
                     <details>Every image is the average of sixteen frames recorded by the direct electron detector</details>
                  </image_recording>
               </image_recording_list>
            </single_particle_microscopy>
         </microscopy_list>
         <singleparticle_processing image_processing_id="1">
            <ctf_correction>
               <details>each particle</details>
            </ctf_correction>
            <final_reconstruction>
               <applied_symmetry>
                  <point_group>C1</point_group>
               </applied_symmetry>
               <resolution res_type="BY AUTHOR" units="&#8491;">5.9</resolution>
               <resolution_method>OTHER</resolution_method>
               <software_list>
                  <software>
                     <name>CTFFIND3, RELION</name>
                  </software>
               </software_list>
               <details>To correct for beam-induced movements, the 16 video frames for each micrograph were first aligned using whole-image motion correction. Second, particle based beam-induced movement correction was performed using statistical movie processing in RELION.</details>
               <number_images_used>179079</number_images_used>
            </final_reconstruction>
         </singleparticle_processing>
      </structure_determination>
   </structure_determination_list>
   <map format="CCP4" size_kbytes="85751">
      <file>emd_2966.map.gz</file>
      <symmetry>
         <space_group>1</space_group>
      </symmetry>
      <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
      <dimensions>
         <col>280</col>
         <row>280</row>
         <sec>280</sec>
      </dimensions>
      <origin>
         <col>0</col>
         <row>0</row>
         <sec>0</sec>
      </origin>
      <spacing>
         <x>280</x>
         <y>280</y>
         <z>280</z>
      </spacing>
      <cell>
         <a units="&#8491;">495.6</a>
         <b units="&#8491;">495.6</b>
         <c units="&#8491;">495.6</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>-0.19736847</minimum>
         <maximum>0.37212843</maximum>
         <average>0.00018776</average>
         <std>0.01347888</std>
      </statistics>
      <pixel_spacing>
         <x units="&#8491;">1.77</x>
         <y units="&#8491;">1.77</y>
         <z units="&#8491;">1.77</z>
      </pixel_spacing>
      <contour_list>
         <contour primary="true">
            <level>0.05</level>
            <source>AUTHOR</source>
         </contour>
      </contour_list>
      <annotation_details>Reconstruction of the yeast U4/U6.U5 tri-snRNP</annotation_details>
      <details>::::EMDATABANK.org::::EMD-2966::::</details>
   </map>
   <interpretation>
      <modelling_list>
         <modelling>
            <initial_model>
               <access_code>4I43</access_code>
            </initial_model>
            <refinement_protocol>RIGID BODY FIT</refinement_protocol>
            <software_list>
               <software>
                  <name>Chimera</name>
               </software>
            </software_list>
            <refinement_space>REAL</refinement_space>
         </modelling>
         <modelling>
            <initial_model>
               <access_code>4BGD</access_code>
            </initial_model>
            <refinement_protocol>RIGID BODY FIT</refinement_protocol>
            <software_list>
               <software>
                  <name>Chimera, coot</name>
               </software>
            </software_list>
            <refinement_space>REAL</refinement_space>
         </modelling>
         <modelling>
            <initial_model>
               <access_code>4WZJ</access_code>
            </initial_model>
            <refinement_protocol>RIGID BODY FIT</refinement_protocol>
            <software_list>
               <software>
                  <name>Chimera</name>
               </software>
            </software_list>
            <refinement_space>REAL</refinement_space>
         </modelling>
         <modelling>
            <initial_model>
               <access_code>1QGV</access_code>
            </initial_model>
            <refinement_protocol>RIGID BODY FIT</refinement_protocol>
            <software_list>
               <software>
                  <name>Chimera</name>
               </software>
            </software_list>
            <refinement_space>REAL</refinement_space>
         </modelling>
         <modelling>
            <initial_model>
               <access_code>2OZB</access_code>
            </initial_model>
            <refinement_protocol>RIGID BODY FIT</refinement_protocol>
            <software_list>
               <software>
                  <name>Chimera</name>
               </software>
            </software_list>
            <refinement_space>REAL</refinement_space>
         </modelling>
         <modelling>
            <initial_model>
               <access_code>2ALE</access_code>
            </initial_model>
            <refinement_protocol>RIGID BODY FIT</refinement_protocol>
            <software_list>
               <software>
                  <name>Chimera</name>
               </software>
            </software_list>
            <refinement_space>REAL</refinement_space>
         </modelling>
         <modelling>
            <initial_model>
               <access_code>4M77</access_code>
            </initial_model>
            <refinement_protocol>RIGID BODY FIT</refinement_protocol>
            <software_list>
               <software>
                  <name>Chimera</name>
               </software>
            </software_list>
            <refinement_space>REAL</refinement_space>
         </modelling>
      </modelling_list>
      <figure_list>
         <figure>
            <file>emd_2966.png</file>
         </figure>
      </figure_list>
   </interpretation>
   <validation>
      <fsc_curve>
         <file>emd_2966_fsc.xml</file>
      </fsc_curve>
   </validation>
</emd>