<emd emdb_id="EMD-5353" version="3.0.1.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="https://github.com/emdb-empiar/emdb-schemas/blob/master/v3/v3_0_1_1/emdb_relaxed.xsd">
    <admin>
        <current_status>
            <code>REL</code>
            <processing_site>RCSB</processing_site>
        </current_status>
        <sites>
            <deposition>RCSB</deposition>
            <last_processing>RCSB</last_processing>
        </sites>
        <key_dates>
            <deposition>2011-11-14</deposition>
            <header_release>2011-11-28</header_release>
            <map_release>2012-01-23</map_release>
            <update>2012-02-07</update>
        </key_dates>
        <title>The 3D volume of the Birnavirus, Espirito Santo Virus.</title>
        <authors_list>
            <author>Vancini R</author>
            <author>Paredes A</author>
            <author>Ribeiro M</author>
            <author>Blackburn K</author>
            <author>Ferreira D</author>
            <author>Kononchik J</author>
            <author>Hernandez R</author>
            <author>Brown D</author>
        </authors_list>
        <keywords>Birnavirus, cryoEM</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Vancini R</author>
                    <author order="2">Paredes A</author>
                    <author order="3">Ribeiro M</author>
                    <author order="4">Blackburn K</author>
                    <author order="5">Ferreira D</author>
                    <author order="6">Kononchik JP</author>
                    <author order="7">Hernandez R</author>
                    <author order="8">Brown D</author>
                    <title>Espirito Santo virus: a new birnavirus that replicates in insect cells.</title>
                    <journal>J.VIROL.</journal>
                    <volume>86</volume>
                    <first_page>2390</first_page>
                    <last_page>2399</last_page>
                    <year>2012</year>
                    <external_references type="PUBMED">22171264</external_references>
                    <external_references type="DOI">doi:10.1128/JVI.06614-11</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>Espirito Santo Virus</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Espirito Santo Virus</name>
                <oligomeric_state>Icosahedral</oligomeric_state>
                <number_unique_components>1</number_unique_components>
            </sample_supramolecule>
            <virus_supramolecule supramolecule_id="1">
                <name synonym="ESV">Espirito Santo virus</name>
                <sci_species_name ncbi="1127767">Espirito Santo virus</sci_species_name>
                <natural_host database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                    <synonym_organism>INVERTEBRATES</synonym_organism>
                </natural_host>
                <host_system database="NCBI" />
                <virus_shell shell_id="1">
                    <diameter units="&#8491;">750</diameter>
                    <triangulation>13</triangulation>
                </virus_shell>
                <virus_type>VIRION</virus_type>
                <virus_isolate>STRAIN</virus_isolate>
                <virus_enveloped>false</virus_enveloped>
                <virus_empty>false</virus_empty>
                <syn_species_name>ESV</syn_species_name>
            </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">
                    <buffer>
                        <ph>7.5</ph>
                        <details>1.5% glutaraldehyde, 20mM HEPES, pH 7.5</details>
                    </buffer>
                    <grid>
                        <details>400 mesh copper grids</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <instrument>HOMEMADE PLUNGER</instrument>
                        <details>Vitrification instrument: Home made plunger. Vitrification carried out using home made lacey carbon films according to previously published protocols</details>
                        <method>Applied specimen to lacey carbon grids, blotted from behind and plunged into cryogen after 2-3 seconds</method>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>FEI POLARA 300</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">2.0</nominal_cs>
                    <nominal_magnification>39000.0</nominal_magnification>
                    <specimen_holder_model>OTHER</specimen_holder_model>
                    <alignment_procedure>
                        <legacy>
                            <astigmatism>corrected using power spectrum</astigmatism>
                        </legacy>
                    </alignment_procedure>
                    <date>2010-06-20</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">TVIPS TEMCAM-F415 (4k x 4k)</film_or_detector_model>
                            <digitization_details>
                                <sampling_interval units="&#181;m">15</sampling_interval>
                            </digitization_details>
                            <number_real_images>199</number_real_images>
                            <bits_per_pixel>16.</bits_per_pixel>
                        </image_recording>
                    </image_recording_list>
                    <specimen_holder>Screw ring cartidge</specimen_holder>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <details>The particles were selected using e2boxer.py in the EMAN2 suite of programs</details>
                <ctf_correction>
                    <details>Each particle</details>
                </ctf_correction>
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">12.0</resolution>
                    <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>EMAN</name>
                        </software>
                    </software_list>
                    <number_images_used>5928</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
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        <file>emd_5353.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>336</col>
            <row>336</row>
            <sec>336</sec>
        </dimensions>
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            <col>-168</col>
            <row>-168</row>
            <sec>-168</sec>
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            <x>336</x>
            <y>336</y>
            <z>336</z>
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            <a units="&#8491;">769.44</a>
            <b units="&#8491;">769.44</b>
            <c units="&#8491;">769.44</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>
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        <statistics>
            <minimum>-8.09881592</minimum>
            <maximum>9.754880910000001</maximum>
            <average>0.14425604</average>
            <std>1.28415811</std>
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        <pixel_spacing>
            <x units="&#8491;">2.29</x>
            <y units="&#8491;">2.29</y>
            <z units="&#8491;">2.29</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>1.28</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>This is the 3D volume of the Birnavirus, Espirito Santo Virus</annotation_details>
        <details>::::EMDATABANK.org::::EMD-5353::::</details>
    </map>
</emd>