<?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_9/emdb.xsd" emdb_id="EMD-10730" version="3.0.1.9">
    <admin>
        <current_status>
            <date>2020-06-17</date>
            <code>REL</code>
            <processing_site>PDBe</processing_site>
        </current_status>
        <sites>
            <deposition>PDBe</deposition>
            <last_processing>PDBe</last_processing>
        </sites>
        <key_dates>
            <deposition>2020-03-05</deposition>
            <header_release>2020-05-06</header_release>
            <map_release>2020-05-06</map_release>
            <update>2020-06-17</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>Medical Research Council (MRC, United Kingdom)</funding_body>
                <code>MC_UP_1201/12</code>
                <country>United Kingdom</country>
            </grant_reference>
        </grant_support>
        <title>Conformation2_Mcm2,5-ssDNA_MultiBody</title>
        <authors_list>
            <author>Baretic D</author>
            <author>Jenkyn-Bedford M</author>
        </authors_list>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Baretic D</author>
                    <author order="2">Jenkyn-Bedford M</author>
                    <author order="3">Aria V</author>
                    <author order="4">Cannone G</author>
                    <author order="5">Skehel M</author>
                    <author order="6">Yeeles JTP</author>
                    <title>Cryo-EM Structure of the Fork Protection Complex Bound to CMG at a Replication Fork.</title>
                    <journal_abbreviation>Mol.Cell</journal_abbreviation>
                    <country>US</country>
                    <volume>78</volume>
                    <first_page>926</first_page>
                    <last_page>940.e13</last_page>
                    <year>2020</year>
                    <external_references type="PUBMED">32369734</external_references>
                    <external_references type="DOI">doi:10.1016/j.molcel.2020.04.012</external_references>
                    <external_references type="ISSN">1097-2765</external_references>
                    <external_references type="CSD">2168</external_references>
                    <external_references type="ASTM">MOCEFL</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-10730</emdb_id>
                <relationship>
                    <other>associated EM volume</other>
                </relationship>
            </emdb_reference>
        </emdb_list>
    </crossreferences>
    <sample>
        <name>Conformation 2 of CMG-Csm3-Tof1-Mrc1-Ctf4 with a fork DNA</name>
        <supramolecule_list>
            <complex_supramolecule supramolecule_id="1">
                <name>Conformation 2 of CMG-Csm3-Tof1-Mrc1-Ctf4 with a fork DNA</name>
                <parent>0</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>1</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>2</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>3</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>4</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>5</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>6</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>7</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <details>Mcm2,5 domains with bound fragment of ssDNA</details>
                <molecular_weight>
                    <theoretical units="MDa">1.4</theoretical>
                </molecular_weight>
            </complex_supramolecule>
            <complex_supramolecule supramolecule_id="2">
                <name>CMG-Csm3-Tof1-Mrc1-Ctf4</name>
                <parent>1</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>1</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>3</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>4</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>5</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>6</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>7</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <natural_source database="NCBI">
                    <organism ncbi="4932">Saccharomyces cerevisiae</organism>
                </natural_source>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="4932">Saccharomyces cerevisiae</recombinant_organism>
                </recombinant_expression>
            </complex_supramolecule>
            <complex_supramolecule supramolecule_id="3">
                <name>DNA</name>
                <parent>1</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>2</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <natural_source database="NCBI">
                    <organism ncbi="32630">synthetic construct</organism>
                </natural_source>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="32630">synthetic construct</recombinant_organism>
                </recombinant_expression>
            </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">0.5</concentration>
                    <buffer>
                        <ph>7.5</ph>
                        <component>
                            <concentration units="mM">25.0</concentration>
                            <formula>HEPES</formula>
                            <name>4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid</name>
                        </component>
                        <component>
                            <concentration units="mM">150.0</concentration>
                            <formula>NaOAc</formula>
                            <name>sodium acetate</name>
                        </component>
                        <component>
                            <concentration units="mM">0.5</concentration>
                            <formula>TCEP</formula>
                            <name>tris(2-carboxyethyl)phosphine</name>
                        </component>
                        <component>
                            <concentration units="mM">0.1</concentration>
                            <formula>AMP-PNP</formula>
                            <name>adenylyl-imidodiphosphate</name>
                        </component>
                        <component>
                            <concentration units="mM">0.7</concentration>
                            <formula>Mg(OAc)2</formula>
                            <name>magnesium acetate</name>
                        </component>
                        <component>
                            <concentration units="%">0.005</concentration>
                            <formula>TWEEN20</formula>
                            <name>Polyoxyethylene (20) sorbitan monolaurate</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">5.0</film_thickness>
                        </support_film>
                        <pretreatment>
                            <type>PLASMA CLEANING</type>
                        </pretreatment>
                        <details>plasma current of 15 mA</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">80</chamber_humidity>
                        <chamber_temperature units="K">277.15</chamber_temperature>
                        <instrument>HOMEMADE PLUNGER</instrument>
                        <details>Three microlitres of sample was applied on a grid and incubated for 15-30 s at 4 degC before manually blotting with filter paper for 10 s and plunge-freezing
in liquid ethane.. </details>
                    </vitrification>
                    <details>In vitro reconstitution from individual components: CMG, Csm3-Tof1, Mrc1, Ctf4 and a DNA fork</details>
                </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>
                    <c2_aperture_diameter units="µm">50.0</c2_aperture_diameter>
                    <nominal_cs units="mm">2.7</nominal_cs>
                    <nominal_defocus_min units="µm">1.4</nominal_defocus_min>
                    <calibrated_defocus_min units="µm">0.5</calibrated_defocus_min>
                    <nominal_defocus_max units="µm">2.6</nominal_defocus_max>
                    <calibrated_defocus_max units="µm">3.0</calibrated_defocus_max>
                    <nominal_magnification>130000.0</nominal_magnification>
                    <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
                    <cooling_holder_cryogen>NITROGEN</cooling_holder_cryogen>
                    <alignment_procedure>
                        <coma_free/>
                    </alignment_procedure>
                    <specialist_optics>
                        <energy_filter>
                            <name>GIF Bioquantum</name>
                            <slit_width units="eV">20</slit_width>
                        </energy_filter>
                    </specialist_optics>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>GATAN K2 QUANTUM (4k x 4k)</film_or_detector_model>
                            <detector_mode>COUNTING</detector_mode>
                            <digitization_details>
                                <frames_per_image>1-20</frames_per_image>
                            </digitization_details>
                            <number_grids_imaged>2</number_grids_imaged>
                            <number_real_images>6682</number_real_images>
                            <average_exposure_time units="s">7.0</average_exposure_time>
                            <average_electron_dose_per_image units="e/Å^2">37.0</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>632000</number_selected>
                </particle_selection>
                <ctf_correction>
                    <software_list>
                        <software>
                            <name>Gctf</name>
                            <version>0.50</version>
                        </software>
                    </software_list>
                </ctf_correction>
                <startup_model type_of_model="PDB ENTRY">
                    <pdb_model>
                        <pdb_id>5U8S</pdb_id>
                    </pdb_model>
                </startup_model>
                <final_reconstruction>
                    <number_classes_used>2</number_classes_used>
                    <applied_symmetry>
                        <point_group>C1</point_group>
                    </applied_symmetry>
                    <algorithm>FOURIER SPACE</algorithm>
                    <resolution units="Å" res_type="BY AUTHOR">3.7</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>3.0</version>
                        </software>
                    </software_list>
                    <number_images_used>184000</number_images_used>
                </final_reconstruction>
                <initial_angle_assignment>
                    <type>MAXIMUM LIKELIHOOD</type>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>3.0</version>
                        </software>
                    </software_list>
                </initial_angle_assignment>
                <final_angle_assignment>
                    <type>MAXIMUM LIKELIHOOD</type>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>3.0</version>
                        </software>
                    </software_list>
                </final_angle_assignment>
                <final_three_d_classification>
                    <number_classes>5</number_classes>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>3.0</version>
                        </software>
                    </software_list>
                </final_three_d_classification>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="186625">
        <file>emd_10730.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>360</col>
            <row>360</row>
            <sec>360</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>360</x>
            <y>360</y>
            <z>360</z>
        </spacing>
        <cell>
            <a units="Å">377.64</a>
            <b units="Å">377.64</b>
            <c units="Å">377.64</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>-0.030374365</minimum>
            <maximum>0.061923128</maximum>
            <average>-0.0002571257</average>
            <std>0.0016520123</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">1.049</x>
            <y units="Å">1.049</y>
            <z units="Å">1.049</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.01</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-10730::::</label>
        <annotation_details>Conformation2-multibody-Mcm2,5-ssDNA</annotation_details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <initial_model>
                    <access_code>5U8S</access_code>
                    <chain>
                        <chain_id>2</chain_id>
                    </chain>
                </initial_model>
                <initial_model>
                    <access_code>5U8S</access_code>
                    <chain>
                        <chain_id>5</chain_id>
                    </chain>
                </initial_model>
                <refinement_protocol>OTHER</refinement_protocol>
                <target_criteria>FSC 0.5</target_criteria>
                <refinement_space>REAL</refinement_space>
                <overall_bvalue>20</overall_bvalue>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>
