<?xml version='1.0' encoding='utf-8'?>
<emd emdb_id="EMD-9754" version="3.0.1.3" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="https://github.com/emdb-empiar/emdb-schemas/blob/master/v3/v3_0_1_3/emdb.xsd">
    <admin>
        <current_status>
            <date>2019-04-03</date>
            <code>REL</code>
            <processing_site>PDBj</processing_site>
        </current_status>
        <sites>
            <deposition>PDBj</deposition>
            <last_processing>PDBj</last_processing>
        </sites>
        <key_dates>
            <deposition>2018-12-19</deposition>
            <header_release>2019-01-16</header_release>
            <map_release>2019-01-16</map_release>
            <update>2019-04-03</update>
        </key_dates>
        <title>Cryo-EM structure of Mud crab tombus-like virus at 3.3 Angstroms resolution</title>
        <authors_list>
            <author>Zhang Q</author>
            <author>Gao Y</author>
        </authors_list>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Gao Y</author>
                    <author order="2">Liu S</author>
                    <author order="3">Huang J</author>
                    <author order="4">Wang Q</author>
                    <author order="5">Li K</author>
                    <author order="6">He J</author>
                    <author order="7">He J</author>
                    <author order="8">Weng S</author>
                    <author order="9">Zhang Q</author>
                    <title>Cryo-electron Microscopy Structures of Novel Viruses from Mud CrabScylla paramamosainwith Multiple Infections.</title>
                    <journal_abbreviation>J. Virol.</journal_abbreviation>
                    <country>US</country>
                    <volume>93</volume>
                    <year>2019</year>
                    <external_references type="PUBMED">30651355</external_references>
                    <external_references type="DOI">doi:10.1128/JVI.02255-18</external_references>
                    <external_references type="ISSN">1098-5514</external_references>
                    <external_references type="CSD">0825</external_references>
                    <external_references type="ASTM">JOVIAM</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-9754</emdb_id>
                <relationship>
                    <other>associated EM volume</other>
                </relationship>
                <details>Cryo-EM structure of Mud crab tombus-like virus at 3.3 Angstroms resolution</details>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-9755</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-9756</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
            </emdb_reference>
        </emdb_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>6izl</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>Viruses</name>
        <supramolecule_list>
            <virus_supramolecule supramolecule_id="1">
                <name>Wenzhou tombus-like virus 18</name>
                <parent>0</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>1</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <sci_species_name ncbi="1923671">Wenzhou tombus-like virus 18</sci_species_name>
                <natural_host database="NCBI">
                    <organism ncbi="85552">Scylla paramamosain</organism>
                </natural_host>
                <virus_shell shell_id="1">
                    <triangulation>3</triangulation>
                </virus_shell>
                <virus_type>VIRION</virus_type>
                <virus_isolate>SPECIES</virus_isolate>
                <virus_enveloped>false</virus_enveloped>
                <virus_empty>false</virus_empty>
            </virus_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>mud crab tombus-like virus</name>
                <natural_source database="NCBI">
                    <organism ncbi="1923671">Wenzhou tombus-like virus 18</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.036813723</theoretical>
                </molecular_weight>
                <number_of_copies>3</number_of_copies>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>MTGSNRRANAGRKTQPKPQRKPRAPRRPKVQNAPRIQQGGGPVPLLESNSNMRQMHNGMTRVVGSDYLGVVSVAGNPADA
AAKVRKVLSVSPSSFPGTRLTQMSDLWERYVFRQFRVRYVPSVPNTLACQVMVYQDTDPQDDPTAIKDADALLRQATAQT
GSQQWNFNSAKVIHLAKRSDNQLYYTGPVKENPRFNQQGVVYFIQVSQALDMNGKPLTADMECGSLYVDWVIDFQTPQVN
PSAVEARLPSAGFFTRQILVNDKLTFAAQASLTVALTALSATPKVWLEGPTRVDLATLGGPGGNLVQIELTRAQPGDYTV
KFVGCDSVTLVSSAPIA</string>
                </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>7.2</ph>
                    </buffer>
                    <grid>
                        <model>Quantifoil R1.2/1.3</model>
                        <material>COPPER</material>
                        <support_film film_type_id="1">
                            <film_material>CARBON</film_material>
                            <film_topology>CONTINUOUS</film_topology>
                        </support_film>
                        <pretreatment>
                            <type>GLOW DISCHARGE</type>
                            <atmosphere>AIR</atmosphere>
                            <pressure units="kPa">101.325</pressure>
                        </pretreatment>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">100</chamber_humidity>
                        <chamber_temperature units="K">293</chamber_temperature>
                        <instrument>FEI VITROBOT MARK IV</instrument>
                        <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_magnification>96000.</nominal_magnification>
                    <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
                    <cooling_holder_cryogen>NITROGEN</cooling_holder_cryogen>
                    <temperature>
                        <temperature_min units="K">90.0</temperature_min>
                        <temperature_max units="K">100.0</temperature_max>
                    </temperature>
                    <alignment_procedure>
                        <coma_free />
                    </alignment_procedure>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>GATAN ULTRASCAN 4000 (4k x 4k)</film_or_detector_model>
                            <digitization_details>
                                <dimensions>
                                    <width units="pixel">4096</width>
                                    <height units="pixel">4096</height>
                                </dimensions>
                                <sampling_interval units="µm">15.0</sampling_interval>
                            </digitization_details>
                            <average_electron_dose_per_image units="e/Å^2">20.0</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>
                <final_reconstruction>
                    <number_classes_used>2</number_classes_used>
                    <applied_symmetry>
                        <point_group>I</point_group>
                    </applied_symmetry>
                    <algorithm>BACK PROJECTION</algorithm>
                    <resolution res_type="BY AUTHOR" units="Å">3.3</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>jspr</name>
                            <version>2014-02-10</version>
                        </software>
                    </software_list>
                    <number_images_used>41941</number_images_used>
                </final_reconstruction>
                <initial_angle_assignment>
                    <type>ANGULAR RECONSTITUTION</type>
                    <software_list>
                        <software>
                            <name>jspr</name>
                            <version>2014-02-10</version>
                        </software>
                    </software_list>
                </initial_angle_assignment>
                <final_angle_assignment>
                    <type>ANGULAR RECONSTITUTION</type>
                    <software_list>
                        <software>
                            <name>jspr</name>
                            <version>2014-02-10</version>
                        </software>
                    </software_list>
                </final_angle_assignment>
                <final_three_d_classification>
                    <number_classes>4</number_classes>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>2.0</version>
                        </software>
                    </software_list>
                </final_three_d_classification>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="442369">
        <file>emd_9754.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">447.84003</a>
            <b units="Å">447.84003</b>
            <c units="Å">447.84003</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>-7.9060407</minimum>
            <maximum>14.174388</maximum>
            <average>-0.0024322476</average>
            <std>0.8975434</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">0.933</x>
            <y units="Å">0.933</y>
            <z units="Å">0.933</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>3.5</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-9754::::</label>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <refinement_protocol>BACKBONE TRACE</refinement_protocol>
                <refinement_space>REAL</refinement_space>
                <overall_bvalue>174.699999999999989</overall_bvalue>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>