<emd emdb_id="EMD-5996" 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>2014-07-07</deposition>
            <header_release>2014-08-13</header_release>
            <map_release>2015-07-08</map_release>
            <update>2015-07-08</update>
        </key_dates>
        <title>Electron cryo-microscopy of chimeric EGFP-VP2 capsid</title>
        <authors_list>
            <author>Pascual E</author>
            <author>Mata CP</author>
            <author>Gomez-Blanco J</author>
            <author>Carrascosa JL</author>
            <author>Caston JR</author>
        </authors_list>
        <keywords>chimeric virus-like particles, IBDV VLP, Cryomicroscopy</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="false">
                    <author order="1">Pascual E</author>
                    <author order="2">Mata CP</author>
                    <author order="3">Gomez-Blanco J</author>
                    <author order="4">Barcena J</author>
                    <author order="5">BLanco E</author>
                    <author order="6">Rodriguez J</author>
                    <author order="7">Nieto A</author>
                    <author order="8">Carrascosa JL</author>
                    <author order="9">Caston JR</author>
                    <title>Structural basis for development of avian virus capsids to display H1N1 influenza virus proteins for induction of protective immunity</title>
                    <journal>To Be Published</journal>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-5997</emdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </emdb_reference>
        </emdb_list>
    </crossreferences>
    <sample>
        <name>Infectious bursal disease virus subviral</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Infectious bursal disease virus subviral</name>
                <oligomeric_state>60 copies of IBDV VP2 mutant arranged into 20 trimers</oligomeric_state>
                <number_unique_components>1</number_unique_components>
                <molecular_weight>
                    <theoretical units="MDa">2.8</theoretical>
                </molecular_weight>
            </sample_supramolecule>
            <virus_supramolecule supramolecule_id="1">
                <name synonym="IBDV">Infectious bursal disease virus chicken/Cuba/Soroa/1998</name>
                <sci_species_name ncbi="645118">Infectious bursal disease virus chicken/Cuba/Soroa/1998</sci_species_name>
                <natural_host database="NCBI">
                    <organism ncbi="9031">Gallus gallus</organism>
                    <synonym_organism>VERTEBRATES</synonym_organism>
                </natural_host>
                <host_system database="NCBI">
                    <recombinant_cell>H5</recombinant_cell>
                </host_system>
                <molecular_weight>
                    <theoretical units="MDa">2.8</theoretical>
                </molecular_weight>
                <virus_shell shell_id="1">
                    <diameter units="&#8491;">700</diameter>
                    <triangulation>13</triangulation>
                </virus_shell>
                <virus_type>VIRUS-LIKE PARTICLE</virus_type>
                <virus_isolate>SPECIES</virus_isolate>
                <virus_enveloped>false</virus_enveloped>
                <virus_empty>true</virus_empty>
                <syn_species_name>IBDV</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>6.2</ph>
                        <details>25 mM PIPES, 150 mM NaCl, 20 mM CaCl2</details>
                    </buffer>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <instrument>OTHER</instrument>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>FEI TECNAI F20</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>
                    <nominal_cs units="mm">2.26</nominal_cs>
                    <nominal_magnification>50000.0</nominal_magnification>
                    <specimen_holder_model>SIDE ENTRY, EUCENTRIC</specimen_holder_model>
                    <specialist_optics>
                        <energy_filter>
                            <name>FEI</name>
                        </energy_filter>
                    </specialist_optics>
                    <date>2011-04-01</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="FILM">KODAK SO-163 FILM</film_or_detector_model>
                            <digitization_details>
                                <scanner>ZEISS SCAI</scanner>
                                <sampling_interval units="&#181;m">14</sampling_interval>
                            </digitization_details>
                            <number_real_images>80</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">10</average_electron_dose_per_image>
                            <bits_per_pixel>8.</bits_per_pixel>
                        </image_recording>
                    </image_recording_list>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">22.7</resolution>
                    <resolution_method>OTHER</resolution_method>
                    <software_list>
                        <software>
                            <name>bshow, xmipp</name>
                        </software>
                    </software_list>
                    <number_images_used>600</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="90428">
        <file>emd_5996.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>285</col>
            <row>285</row>
            <sec>285</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>285</x>
            <y>285</y>
            <z>285</z>
        </spacing>
        <cell>
            <a units="&#8491;">798.0</a>
            <b units="&#8491;">798.0</b>
            <c units="&#8491;">798.0</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>-0.01409956</minimum>
            <maximum>0.02120063</maximum>
            <average>0.00036926</average>
            <std>0.00378921</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">2.8</x>
            <y units="&#8491;">2.8</y>
            <z units="&#8491;">2.8</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.005</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Reconstruction of mutant IBDV (chimeric EGFP-VP2 capsid)</annotation_details>
        <details>::::EMDATABANK.org::::EMD-5996::::</details>
    </map>
    <interpretation>
        <figure_list>
            <figure>
                <file>emd_5996.png</file>
            </figure>
        </figure_list>
    </interpretation>
</emd>