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    <admin>
        <current_status>
            <date>2021-02-03</date>
            <code>REL</code>
            <processing_site>RCSB</processing_site>
        </current_status>
        <sites>
            <deposition>RCSB</deposition>
            <last_processing>RCSB</last_processing>
        </sites>
        <key_dates>
            <deposition>2017-02-10</deposition>
            <header_release>2017-02-22</header_release>
            <map_release>2017-02-22</map_release>
            <update>2021-02-03</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>AAAS</funding_body>
                <code>Marion Milligan Mason Award</code>
                <country>United States</country>
            </grant_reference>
        </grant_support>
        <title>Samba Virus tomogram</title>
        <authors_list>
            <author>Schrad JR</author>
            <author>Young EJ</author>
            <author>Abrahao JS</author>
            <author>Cortines JR</author>
            <author>Parent KN</author>
        </authors_list>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Schrad JR</author>
                    <author order="2">Young EJ</author>
                    <author order="3">Abrahao JS</author>
                    <author order="4">Cortines JR</author>
                    <author order="5">Parent KN</author>
                    <title>Microscopic Characterization of the Brazilian Giant Samba Virus.</title>
                    <journal_abbreviation>Viruses</journal_abbreviation>
                    <volume>9</volume>
                    <year>2017</year>
                    <external_references type="PUBMED">28216551</external_references>
                    <external_references type="DOI">doi:10.3390/v9020030</external_references>
                    <external_references type="ISSN">1999-4915</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-8599</emdb_id>
                <relationship>
                    <other>associated EM volume</other>
                </relationship>
            </emdb_reference>
        </emdb_list>
    </crossreferences>
    <sample>
        <name>Samba virus</name>
        <supramolecule_list>
            <virus_supramolecule supramolecule_id="1">
                <name>Samba virus</name>
                <parent>0</parent>
                <sci_species_name ncbi="1461100">Samba virus</sci_species_name>
                <natural_host database="NCBI">
                    <organism ncbi="5755">Acanthamoeba castellanii</organism>
                </natural_host>
                <virus_shell shell_id="1">
                    <diameter units="Å">8400.0</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>tomography</method>
            <aggregation_state>particle</aggregation_state>
            <specimen_preparation_list>
                <tomography_preparation preparation_id="1">
                    <buffer>
                        <ph>7.4</ph>
                        <component>
                            <concentration units="mM">20.0</concentration>
                            <name>sodium phosphate</name>
                        </component>
                    </buffer>
                    <grid>
                        <model>Quantifoil 3.5/1</model>
                        <material>COPPER</material>
                        <mesh>300</mesh>
                        <pretreatment>
                            <type>PLASMA CLEANING</type>
                        </pretreatment>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <instrument>HOMEMADE PLUNGER</instrument>
                    </vitrification>
                    <fiducial_markers_list>
                        <fiducial_marker>
                            <manufacturer>Aldrich</manufacturer>
                            <diameter units="nanometer">10</diameter>
                        </fiducial_marker>
                    </fiducial_markers_list>
                    <sectioning>
                        <other_sectioning>NO SECTIONING</other_sectioning>
                    </sectioning>
                </tomography_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <tomography_microscopy microscopy_id="1">
                    <microscope>JEOL 2200FS</microscope>
                    <illumination_mode>FLOOD BEAM</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>FIELD EMISSION GUN</electron_source>
                    <acceleration_voltage units="kV">200</acceleration_voltage>
                    <c2_aperture_diameter units="µm">100.0</c2_aperture_diameter>
                    <nominal_cs units="mm">1.4</nominal_cs>
                    <calibrated_defocus_max units="µm">25.0</calibrated_defocus_max>
                    <nominal_magnification>4000.0</nominal_magnification>
                    <specimen_holder_model>GATAN 914 HIGH TILT LIQUID NITROGEN CRYO TRANSFER TOMOGRAPHY HOLDER</specimen_holder_model>
                    <cooling_holder_cryogen>NITROGEN</cooling_holder_cryogen>
                    <temperature>
                        <temperature_min units="K">83.0</temperature_min>
                        <temperature_max units="K">83.0</temperature_max>
                    </temperature>
                    <alignment_procedure>
                        <basic/>
                    </alignment_procedure>
                    <specialist_optics>
                        <energy_filter>
                            <name>In-column Omega Filter</name>
                        </energy_filter>
                    </specialist_optics>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>DIRECT ELECTRON DE-20 (5k x 3k)</film_or_detector_model>
                            <detector_mode>INTEGRATING</detector_mode>
                            <digitization_details>
                                <dimensions>
                                    <width units="pixel">5120</width>
                                    <height units="pixel">3840</height>
                                </dimensions>
                                <sampling_interval units="µm">6.4</sampling_interval>
                                <frames_per_image>1-45</frames_per_image>
                            </digitization_details>
                            <number_grids_imaged>17</number_grids_imaged>
                            <average_exposure_time units="s">3.0</average_exposure_time>
                            <average_electron_dose_per_image units="e/Å^2">1.1</average_electron_dose_per_image>
                            <details>63 tilt series were collected. From these, 20 complete tomograms were produced, capturing 34 particles.</details>
                        </image_recording>
                    </image_recording_list>
                </tomography_microscopy>
            </microscopy_list>
            <tomography_processing image_processing_id="1">
                <image_recording_id>1</image_recording_id>
                <details>The selected images were motion-corrected and corrected for the gain and dark references prior to performance of the tomographic reconstructions.</details>
                <final_reconstruction>
                    <algorithm>SIMULTANEOUS ITERATIVE (SIRT)</algorithm>
                    <software_list>
                        <software>
                            <name>IMOD</name>
                            <version>4.7.15</version>
                        </software>
                    </software_list>
                    <number_images_used>67</number_images_used>
                </final_reconstruction>
            </tomography_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="293372">
        <file>emd_8599.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>575</col>
            <row>557</row>
            <sec>229</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>575</x>
            <y>557</y>
            <z>229</z>
        </spacing>
        <cell>
            <a units="Å">8452.5</a>
            <b units="Å">8187.9</b>
            <c units="Å">3366.3</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>-587884.1</minimum>
            <maximum>527176.7</maximum>
            <average>-11709.452</average>
            <std>16132.14</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">14.7</x>
            <y units="Å">14.7</y>
            <z units="Å">14.7</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-8599::::</label>
        <annotation_details>Samba Virus particle</annotation_details>
    </map>
    <interpretation>
        <additional_map_list>
            <additional_map format="CCP4" size_kbytes="293372">
                <file>emd_8599_additional_1.map.gz</file>
                <symmetry>
                    <space_group>1</space_group>
                </symmetry>
                <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
                <dimensions>
                    <col>575</col>
                    <row>557</row>
                    <sec>229</sec>
                </dimensions>
                <origin>
                    <col>0</col>
                    <row>0</row>
                    <sec>0</sec>
                </origin>
                <spacing>
                    <x>575</x>
                    <y>557</y>
                    <z>229</z>
                </spacing>
                <cell>
                    <a units="Å">8452.5</a>
                    <b units="Å">8187.9</b>
                    <c units="Å">3366.3</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>-527176.7</minimum>
                    <maximum>587884.1</maximum>
                    <average>11709.452</average>
                    <std>16132.14</std>
                </statistics>
                <pixel_spacing>
                    <x units="Å">14.7</x>
                    <y units="Å">14.7</y>
                    <z units="Å">14.7</z>
                </pixel_spacing>
                <contour_list>
                    <contour primary="true">
                        <source>EMDB</source>
                    </contour>
                </contour_list>
                <label>::::EMDATABANK.org::::EMD-8599::::</label>
                <annotation_details>Samba Virus particle, inverted map</annotation_details>
            </additional_map>
        </additional_map_list>
    </interpretation>
</emd>
