<?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-20593" version="3.0.1.5">
    <admin>
        <current_status>
            <date>2019-09-11</date>
            <code>REL</code>
            <processing_site>RCSB</processing_site>
        </current_status>
        <sites>
            <deposition>RCSB</deposition>
            <last_processing>RCSB</last_processing>
        </sites>
        <key_dates>
            <deposition>2019-08-13</deposition>
            <header_release>2019-08-28</header_release>
            <map_release>2019-09-11</map_release>
            <update>2019-09-11</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>National Institutes of Health/National Cancer Institute</funding_body>
                <code>R01CA193578</code>
                <country>United States</country>
            </grant_reference>
            <grant_reference>
                <funding_body>National Institutes of Health/National Institute Of Allergy and Infectious Diseases</funding_body>
                <code>R01AI116815</code>
                <country>United States</country>
            </grant_reference>
        </grant_support>
        <title>Rotavirus, transcriptionally active</title>
        <authors_list>
            <author>Kelly DF</author>
            <author>Hauser M</author>
        </authors_list>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Hauser M</author>
                    <author order="2">Dearnaley WJ</author>
                    <author order="3">Varano AC</author>
                    <author order="4">Casasanta M</author>
                    <author order="5">McDonald SM</author>
                    <author order="6">Kelly DF</author>
                    <title>Cryo-EM Reveals Architectural Diversity in Active Rotavirus Particles.</title>
                    <journal_abbreviation>Comput Struct Biotechnol J</journal_abbreviation>
                    <volume>17</volume>
                    <first_page>1178</first_page>
                    <last_page>1183</last_page>
                    <year>2019</year>
                    <external_references type="PUBMED">31467657</external_references>
                    <external_references type="DOI">doi:10.1016/j.csbj.2019.07.019</external_references>
                    <external_references type="ISSN">2001-0370</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-20593</emdb_id>
                <relationship>
                    <other>associated EM volume</other>
                </relationship>
            </emdb_reference>
        </emdb_list>
    </crossreferences>
    <sample>
        <name>Simian rotavirus A/SA11-4F</name>
        <supramolecule_list>
            <virus_supramolecule supramolecule_id="1">
                <name>Simian rotavirus A/SA11-4F</name>
                <parent>0</parent>
                <details>Simian Rotavirus double-layered particle assemblies purified using isopycnic centrifugation in cesium chloride</details>
                <sci_species_name ncbi="36436">Simian rotavirus A/SA11-4F</sci_species_name>
                <natural_host database="NCBI">
                    <organism ncbi="36436">Simian rotavirus A/SA11-4F</organism>
                </natural_host>
                <virus_shell shell_id="1">
                    <name>VP6</name>
                    <diameter units="Å">800.0</diameter>
                </virus_shell>
                <virus_type>VIRION</virus_type>
                <virus_isolate>STRAIN</virus_isolate>
                <virus_enveloped>false</virus_enveloped>
                <virus_empty>false</virus_empty>
            </virus_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</concentration>
                    <buffer>
                        <ph>7.5</ph>
                        <details>50mM HEPES, pH7.5, 150mM NaCl, 10mM MgCl2 and 10mM CaCl2</details>
                    </buffer>
                    <grid>
                        <details>Functionalized with Nickle-nitrilotriacetic acid (ni-NTA) monolayers composed of 25% Ni-NTA lipids and 75% 1,2-dilaurylphosphatidylchlorine filler lipids (Avanti Polar lipids)</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">90</chamber_humidity>
                        <chamber_temperature units="K">298</chamber_temperature>
                        <instrument>FEI VITROBOT MARK III</instrument>
                        <details>Sample was frozen on C-flat holey carbon grids. </details>
                    </vitrification>
                    <details>sample was monodispersed</details>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>FEI TECNAI SPIRIT</microscope>
                    <illumination_mode>FLOOD BEAM</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>FIELD EMISSION GUN</electron_source>
                    <acceleration_voltage units="kV">120</acceleration_voltage>
                    <nominal_cs units="mm">2.0</nominal_cs>
                    <nominal_defocus_min units="µm">-1.5</nominal_defocus_min>
                    <nominal_magnification>68000.</nominal_magnification>
                    <specimen_holder_model>SIDE ENTRY, EUCENTRIC</specimen_holder_model>
                    <cooling_holder_cryogen>NITROGEN</cooling_holder_cryogen>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>FEI EAGLE (2k x 2k)</film_or_detector_model>
                            <average_electron_dose_per_image units="e/Å^2">5.0</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>467</number_selected>
                </particle_selection>
                <ctf_correction>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>2.0</version>
                        </software>
                    </software_list>
                </ctf_correction>
                <startup_model type_of_model="OTHER">
                    <details>DLP density map deposited on the Grigorieff website</details>
                </startup_model>
                <final_reconstruction>
                    <number_classes_used>1</number_classes_used>
                    <algorithm>BACK PROJECTION</algorithm>
                    <resolution units="Å" res_type="BY AUTHOR">12.0</resolution>
                    <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>2.0</version>
                        </software>
                    </software_list>
                    <number_images_used>467</number_images_used>
                </final_reconstruction>
                <initial_angle_assignment>
                    <type>OTHER</type>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>2.0</version>
                        </software>
                    </software_list>
                    <details>RELION software package</details>
                </initial_angle_assignment>
                <final_angle_assignment>
                    <type>OTHER</type>
                    <details>RELION software package</details>
                </final_angle_assignment>
                <final_three_d_classification>
                    <number_classes>3</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="32001">
        <file>emd_20593.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>200</col>
            <row>200</row>
            <sec>200</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>200</x>
            <y>200</y>
            <z>200</z>
        </spacing>
        <cell>
            <a units="Å">880.0</a>
            <b units="Å">880.0</b>
            <c units="Å">880.0</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>-0.016788542</minimum>
            <maximum>0.10787897</maximum>
            <average>0.019129312</average>
            <std>0.03691989</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">4.4</x>
            <y units="Å">4.4</y>
            <z units="Å">4.4</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.0812</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-20593::::</label>
        <annotation_details>Rotavirus actively transcribing</annotation_details>
    </map>
</emd>
