<?xml version="1.0" encoding="UTF-8"?>
<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="https://github.com/emdb-empiar/emdb-schemas/blob/master/v3/v3_0_1_5/emdb.xsd" emdb_id="EMD-10140" version="3.0.1.5">
    <admin>
        <current_status>
            <date>2019-09-18</date>
            <code>REL</code>
            <processing_site>PDBe</processing_site>
        </current_status>
        <sites>
            <deposition>PDBe</deposition>
            <last_processing>PDBe</last_processing>
        </sites>
        <key_dates>
            <deposition>2019-07-23</deposition>
            <header_release>2019-07-31</header_release>
            <map_release>2019-07-31</map_release>
            <update>2019-09-18</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>Medical Research Council (United Kingdom)</funding_body>
                <code>MC_U105184330</code>
                <country>United Kingdom</country>
            </grant_reference>
            <grant_reference>
                <funding_body>European Research Council</funding_body>
                <code>AdG-693087-SPLICE3D</code>
                <country>Belgium</country>
            </grant_reference>
        </grant_support>
        <title>Post-catalytic P complex spliceosome at 3.3 angstrom resolution from merging data sets</title>
        <authors_list>
            <author>Wilkinson ME</author>
            <author>Nagai K</author>
        </authors_list>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Wilkinson ME</author>
                    <author order="2">Kumar A</author>
                    <author order="3">Casanal A</author>
                    <title>Methods for merging data sets in electron cryo-microscopy.</title>
                    <journal_abbreviation>Acta Crystallogr D Struct Biol</journal_abbreviation>
                    <volume>75</volume>
                    <first_page>782</first_page>
                    <last_page>791</last_page>
                    <year>2019</year>
                    <external_references type="PUBMED">31478901</external_references>
                    <external_references type="DOI">doi:10.1107/S2059798319010519</external_references>
                    <external_references type="ISSN">2059-7983</external_references>
                </journal_citation>
            </primary_citation>
            <secondary_citation>
                <journal_citation published="true">
                    <author order="4">Wilkinson ME</author>
                    <author order="5">Fica SM</author>
                    <author order="6">Galej WP</author>
                    <author order="7">Norman CM</author>
                    <author order="8">Newman AJ</author>
                    <author order="9">Nagai K</author>
                    <title>Postcatalytic spliceosome structure reveals mechanism of 3'-splice site selection.</title>
                    <journal_abbreviation>Science</journal_abbreviation>
                    <country>US</country>
                    <volume>358</volume>
                    <first_page>1283</first_page>
                    <last_page>1288</last_page>
                    <year>2017</year>
                    <external_references type="PUBMED">29146871</external_references>
                    <external_references type="DOI">doi:10.1126/science.aar3729</external_references>
                    <external_references type="ISSN">1095-9203</external_references>
                    <external_references type="CSD">0038</external_references>
                    <external_references type="ASTM">SCIEAS</external_references>
                </journal_citation>
            </secondary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-10140</emdb_id>
                <relationship>
                    <other>associated EM volume</other>
                </relationship>
            </emdb_reference>
        </emdb_list>
    </crossreferences>
    <sample>
        <name>P complex spliceosome with 3' exon docked</name>
        <supramolecule_list>
            <complex_supramolecule supramolecule_id="1">
                <name>P complex spliceosome with 3' exon docked</name>
                <parent>0</parent>
                <natural_source database="NCBI">
                    <organism ncbi="4932">Saccharomyces cerevisiae</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">2.2</theoretical>
                </molecular_weight>
            </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">1.4</concentration>
                    <buffer>
                        <ph>7.8</ph>
                        <component>
                            <concentration units="mM">20.0</concentration>
                            <name>HEPES</name>
                        </component>
                        <component>
                            <concentration units="mM">75.0</concentration>
                            <formula>KCl</formula>
                        </component>
                        <component>
                            <concentration units="mM">0.25</concentration>
                            <name>EDTA</name>
                        </component>
                    </buffer>
                    <grid>
                        <model>Quantifoil R2/2</model>
                        <material>COPPER</material>
                        <mesh>400</mesh>
                        <support_film film_type_id="1">
                            <film_material>CARBON</film_material>
                            <film_topology>CONTINUOUS</film_topology>
                            <film_thickness units="nm">7.0</film_thickness>
                        </support_film>
                        <pretreatment>
                            <type>GLOW DISCHARGE</type>
                            <atmosphere>AIR</atmosphere>
                        </pretreatment>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">100</chamber_humidity>
                        <chamber_temperature units="K">277</chamber_temperature>
                        <instrument>FEI VITROBOT MARK III</instrument>
                        <details>3 uL sample was applied to the grid, left for 30s, then blotted for 3s and immediately plunged into liquid ethane. </details>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>FEI TITAN KRIOS</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">2.7</nominal_cs>
                    <nominal_defocus_min units="µm">0.2</nominal_defocus_min>
                    <nominal_defocus_max units="µm">3.0</nominal_defocus_max>
                    <nominal_magnification>105000.</nominal_magnification>
                    <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
                    <cooling_holder_cryogen>NITROGEN</cooling_holder_cryogen>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>GATAN K2 SUMMIT (4k x 4k)</film_or_detector_model>
                            <detector_mode>COUNTING</detector_mode>
                            <number_grids_imaged>1</number_grids_imaged>
                            <number_real_images>2384</number_real_images>
                            <average_exposure_time units="s">12.0</average_exposure_time>
                            <average_electron_dose_per_image units="e/Å^2">47.0</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                </single_particle_microscopy>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>FEI TITAN KRIOS</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">2.7</nominal_cs>
                    <nominal_magnification>130000.</nominal_magnification>
                    <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
                    <cooling_holder_cryogen>NITROGEN</cooling_holder_cryogen>
                    <image_recording_list>
                        <image_recording image_recording_id="2">
                            <film_or_detector_model>GATAN K2 SUMMIT (4k x 4k)</film_or_detector_model>
                            <detector_mode>SUPER-RESOLUTION</detector_mode>
                            <number_grids_imaged>1</number_grids_imaged>
                            <number_real_images>173</number_real_images>
                            <average_exposure_time units="s">7.0</average_exposure_time>
                            <average_electron_dose_per_image units="e/Å^2">45.0</average_electron_dose_per_image>
                        </image_recording>
                        <image_recording image_recording_id="3">
                            <film_or_detector_model>GATAN K2 SUMMIT (4k x 4k)</film_or_detector_model>
                            <detector_mode>COUNTING</detector_mode>
                            <digitization_details>
                                <frames_per_image>1-35</frames_per_image>
                            </digitization_details>
                            <number_grids_imaged>1</number_grids_imaged>
                            <number_real_images>1441</number_real_images>
                            <average_exposure_time units="s">7.0</average_exposure_time>
                            <average_electron_dose_per_image units="e/Å^2">45.0</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <image_recording_id>1</image_recording_id>
                <particle_selection>
                    <number_selected>286038</number_selected>
                </particle_selection>
                <startup_model type_of_model="EMDB MAP">
                    <emdb_id>EMD-3979</emdb_id>
                </startup_model>
                <final_reconstruction>
                    <applied_symmetry>
                        <point_group>C1</point_group>
                    </applied_symmetry>
                    <resolution units="Å" res_type="BY AUTHOR">3.3</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <number_images_used>52748</number_images_used>
                </final_reconstruction>
                <initial_angle_assignment>
                    <type>MAXIMUM LIKELIHOOD</type>
                </initial_angle_assignment>
                <final_angle_assignment>
                    <type>MAXIMUM LIKELIHOOD</type>
                </final_angle_assignment>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="442369">
        <file>emd_10140.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>480</col>
            <row>480</row>
            <sec>480</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>480</x>
            <y>480</y>
            <z>480</z>
        </spacing>
        <cell>
            <a units="Å">537.6</a>
            <b units="Å">537.6</b>
            <c units="Å">537.6</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>-0.06356835</minimum>
            <maximum>0.11250346</maximum>
            <average>0.000039320665</average>
            <std>0.0037345937</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">1.12</x>
            <y units="Å">1.12</y>
            <z units="Å">1.12</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.023</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-10140::::</label>
        <annotation_details>None</annotation_details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <initial_model>
                    <access_code>6EXN</access_code>
                </initial_model>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>
