<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" emdb_id="EMD-8265" version="3.0.0.0" xsi:schemaLocation="https://github.com/emdb-empiar/emdb-schemas/blob/master/v3/v3_0_0_0/emdb.xsd">
    <admin>
        <current_status>
            <date>2018-07-18</date>
            <code>REL</code>
            <processing_site>RCSB</processing_site>
        </current_status>
        <sites>
            <deposition>RCSB</deposition>
            <last_processing>RCSB</last_processing>
        </sites>
        <key_dates>
            <deposition>2016-06-25</deposition>
            <header_release>2016-07-06</header_release>
            <map_release>2016-07-06</map_release>
            <update>2018-07-18</update>
        </key_dates>
        <title>CIP-treated Brome Mosaic Virus (RNA2.3/4)</title>
        <authors_list>
            <author>Hoover HS</author>
            <author>Wang JC-Y</author>
            <author>Middleton S</author>
            <author>Ni P</author>
            <author>Zlotnick A</author>
            <author>Vaughan RC</author>
            <author>Kao CC</author>
        </authors_list>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Hoover HS</author>
                    <author order="2">Wang JC</author>
                    <author order="3">Middleton S</author>
                    <author order="4">Ni P</author>
                    <author order="5">Zlotnick A</author>
                    <author order="6">Vaughan RC</author>
                    <author order="7">Kao CC</author>
                    <title>Phosphorylation of the Brome Mosaic Virus Capsid Regulates the Timing of Viral Infection.</title>
                    <journal_abbreviation>J.Virol.</journal_abbreviation>
                    <country>US</country>
                    <volume>90</volume>
                    <first_page>7748</first_page>
                    <last_page>7760</last_page>
                    <year>2016</year>
                    <external_references type="PUBMED">27334588</external_references>
                    <external_references type="DOI">doi:10.1128/JVI.00833-16</external_references>
                    <external_references type="ISSN">1098-5514</external_references>
                    <external_references type="CSD">0825</external_references>
                    <external_references type="ASTM">JOVIAM</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-8265</emdb_id>
                <relationship>
                    <other>associated EM volume</other>
                </relationship>
                <details>BMV B2.3/4 CIP-treated</details>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-8262</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
                <details>BMV B1 Mock-treated</details>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-8263</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
                <details>BMV B1 CIP-treated</details>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-8264</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
                <details>BMV B2.3/4 Mock-treated</details>
            </emdb_reference>
        </emdb_list>
    </crossreferences>
    <sample>
        <name>Brome mosaic virus</name>
        <supramolecule_list>
            <virus_supramolecule supramolecule_id="1">
                <name>Brome mosaic virus</name>
                <parent>0</parent>
                <details>BMV B2.3/4 CIP-treated</details>
                <sci_species_name ncbi="12302">Brome mosaic virus</sci_species_name>
                <natural_host database="NCBI">
                    <organism ncbi="4565">Triticum aestivum</organism>
                </natural_host>
                <molecular_weight>
                    <theoretical units="MDa">4.6</theoretical>
                </molecular_weight>
                <virus_shell shell_id="1">
                    <name>Capsid</name>
                    <diameter units="&#8491;">280.0</diameter>
                    <triangulation>3</triangulation>
                </virus_shell>
                <virus_type>VIRION</virus_type>
                <virus_isolate>SPECIES</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">0.5</concentration>
                    <buffer>
                        <ph>5.2</ph>
                        <details>250 mM NaOAc and 10 mM MgCl2 (pH 5.2)
+ 10 units of calf intestinal phosphatase (CIP)</details>
                    </buffer>
                    <grid>
                        <model>Quantifoil R2/2</model>
                        <material>COPPER</material>
                        <mesh>200</mesh>
                        <support_film film_type_id="1">
                            <film_material>CARBON</film_material>
                            <film_topology>HOLEY</film_topology>
                        </support_film>
                        <pretreatment>
                            <type>GLOW DISCHARGE</type>
                        </pretreatment>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">100</chamber_humidity>
                        <chamber_temperature units="K">278</chamber_temperature>
                        <instrument>FEI VITROBOT MARK III</instrument>
                        <details />
                    </vitrification>
                    <details>0.5-1 mg/ml</details>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>JEOL 3200FS</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">1.1</nominal_cs>
                    <nominal_defocus_min units="&#181;m">0.7</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">3.5</nominal_defocus_max>
                    <nominal_magnification>80000.</nominal_magnification>
                    <specimen_holder_model>GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER</specimen_holder_model>
                    <cooling_holder_cryogen>NITROGEN</cooling_holder_cryogen>
                    <temperature>
                        <temperature_min units="K">97.0</temperature_min>
                    </temperature>
                    <alignment_procedure>
                        <basic />
                    </alignment_procedure>
                    <specialist_optics>
                        <energy_filter>
                            <name>In-column Omega Filter</name>
                            <lower_energy_threshold units="eV">0</lower_energy_threshold>
                            <upper_energy_threshold units="eV">20</upper_energy_threshold>
                        </energy_filter>
                    </specialist_optics>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>GATAN ULTRASCAN 4000 (4k x 4k)</film_or_detector_model>
                            <digitization_details>
                                <dimensions>
                                    <width units="pixel">4096</width>
                                    <height units="pixel">4096</height>
                                </dimensions>
                                <sampling_interval units="&#181;m">15.0</sampling_interval>
                            </digitization_details>
                            <average_exposure_time units="s">0.5</average_exposure_time>
                            <average_electron_dose_per_image units="e/&#8491;^2">20.0</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>19834</number_selected>
                </particle_selection>
                <ctf_correction>
                    <software_list>
                        <software>
                            <name>CTFFIND</name>
                            <version>3</version>
                        </software>
                    </software_list>
                </ctf_correction>
                <startup_model type_of_model="OTHER">
                    <details>de novo model building in AUTO3DEM</details>
                </startup_model>
                <final_reconstruction>
                    <applied_symmetry>
                        <point_group>I</point_group>
                    </applied_symmetry>
                    <resolution res_type="BY AUTHOR" units="&#8491;">8.1</resolution>
                    <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>Auto3DEM</name>
                            <version>4.04</version>
                        </software>
                    </software_list>
                    <number_images_used>13882</number_images_used>
                </final_reconstruction>
                <initial_angle_assignment>
                    <type>RANDOM ASSIGNMENT</type>
                    <software_list>
                        <software>
                            <name>Auto3DEM</name>
                            <version>4.04</version>
                        </software>
                    </software_list>
                </initial_angle_assignment>
                <final_angle_assignment>
                    <type>PROJECTION MATCHING</type>
                    <projection_matching_processing />
                    <software_list>
                        <software>
                            <name>Auto3DEM</name>
                            <version>4.04</version>
                        </software>
                    </software_list>
                </final_angle_assignment>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="109084">
        <file>emd_8265.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>301</col>
            <row>301</row>
            <sec>301</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>301</x>
            <y>301</y>
            <z>301</z>
        </spacing>
        <cell>
            <a units="&#8491;">455.112</a>
            <b units="&#8491;">455.112</b>
            <c units="&#8491;">455.112</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>-0.1662818</minimum>
            <maximum>0.6168169</maximum>
            <average>0.01195478</average>
            <std>0.076429024</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">1.512</x>
            <y units="&#8491;">1.512</y>
            <z units="&#8491;">1.512</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.13</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-8265::::</label>
        <annotation_details>Cryo-EM density map of BMV (B2.3/4 CIP-treated)</annotation_details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <refinement_protocol>RIGID BODY FIT</refinement_protocol>
                <refinement_space>REAL</refinement_space>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>