<emd emdb_id="EMD-6000" 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>2014-07-10</deposition>
            <header_release>2014-08-20</header_release>
            <map_release>2014-09-10</map_release>
            <update>2016-02-17</update>
        </key_dates>
        <title>Full virus map of Brome Mosaic Virus</title>
        <authors_list>
            <author>Wang Z</author>
            <author>Hryc FC</author>
            <author>Bammes B</author>
            <author>Afonine PV</author>
            <author>Jakana J</author>
            <author>Chen DH</author>
            <author>Liu XA</author>
            <author>Baker ML</author>
            <author>Kao C</author>
            <author>Ludtke SJ</author>
            <author>Schmid MF</author>
            <author>Adams PD</author>
            <author>Chiu W</author>
        </authors_list>
        <keywords />
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Wang Z</author>
                    <author order="2">Hryc CF</author>
                    <author order="3">Bammes B</author>
                    <author order="4">Afonine PV</author>
                    <author order="5">Jakana J</author>
                    <author order="6">Chen DH</author>
                    <author order="7">Liu X</author>
                    <author order="8">Baker ML</author>
                    <author order="9">Kao C</author>
                    <author order="10">Ludtke SJ</author>
                    <author order="11">Schmid MF</author>
                    <author order="12">Adams PD</author>
                    <author order="13">Chiu W</author>
                    <title>An atomic model of brome mosaic virus using direct electron detection and real-space optimization</title>
                    <journal>Nature Communications</journal>
                    <volume>5</volume>
                    <first_page>4808</first_page>
                    <last_page>4808</last_page>
                    <year>2014</year>
                    <external_references type="PUBMED">25185801</external_references>
                    <external_references type="DOI">doi:10.1038/ncomms5808</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>3j7l</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
            <pdb_reference>
                <pdb_id>3j7m</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
            <pdb_reference>
                <pdb_id>3j7n</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
        <auxiliary_link_list>
            <auxiliary_link>
                <link>http://dx.doi.org/10.6019/EMPIAR-10010</link>
            </auxiliary_link>
        </auxiliary_link_list>
    </crossreferences>
    <sample>
        <name>brome mosaic virus</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>brome mosaic virus</name>
                <number_unique_components>1</number_unique_components>
                <molecular_weight>
                    <theoretical units="MDa">4.6</theoretical>
                </molecular_weight>
            </sample_supramolecule>
            <virus_supramolecule supramolecule_id="1">
                <name>Brome mosaic virus</name>
                <sci_species_name ncbi="12302">Brome mosaic virus</sci_species_name>
                <natural_host database="NCBI">
                    <organism ncbi="4565">Triticum aestivum</organism>
                    <synonym_organism>PLANTAE(HIGHER PLANTS)</synonym_organism>
                </natural_host>
                <host_system database="NCBI" />
                <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">
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">100</chamber_humidity>
                        <chamber_temperature units="K">171.0</chamber_temperature>
                        <instrument>FEI VITROBOT MARK IV</instrument>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>JEOL 3200FSC</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_defocus_min units="&#181;m">0.5</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">2.0</nominal_defocus_max>
                    <nominal_magnification>50000.0</nominal_magnification>
                    <specimen_holder_model>JEOL 3200FSC CRYOHOLDER</specimen_holder_model>
                    <date>2013-01-10</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">DIRECT ELECTRON DE-12 (4k x 3k)</film_or_detector_model>
                        </image_recording>
                    </image_recording_list>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <final_reconstruction>
                    <resolution res_type="BY AUTHOR" units="&#8491;">3.8</resolution>
                    <resolution_method>OTHER</resolution_method>
                    <software_list>
                        <software>
                            <name>MPSA, EMAN</name>
                        </software>
                    </software_list>
                    <number_images_used>30000</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
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        <file>emd_6000.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>420</col>
            <row>420</row>
            <sec>420</sec>
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        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
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        <spacing>
            <x>420</x>
            <y>420</y>
            <z>420</z>
        </spacing>
        <cell>
            <a units="&#8491;">415.8</a>
            <b units="&#8491;">415.8</b>
            <c units="&#8491;">415.8</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>-10.33948612</minimum>
            <maximum>17.469449999999998</maximum>
            <average>0.00000003</average>
            <std>1.11417329</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">0.99</x>
            <y units="&#8491;">0.99</y>
            <z units="&#8491;">0.99</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>5.0</level>
                <source>EMDB</source>
            </contour>
        </contour_list>
        <annotation_details>full BMV map with combined data</annotation_details>
        <details>::::EMDATABANK.org::::EMD-6000::::</details>
    </map>
</emd>