<?xml version="1.0" encoding="UTF-8"?>
<emd emdb_id="EMD-3000" version="3.0.1.9">
    <admin>
        <status_history_list>
            <status status_id="1">
                <code>HPUB</code>
            </status>
        </status_history_list>
        <current_status>
            <code superseded="true">OBS</code>
            <processing_site>PDBe</processing_site>
        </current_status>
        <sites>
            <deposition>PDBe</deposition>
            <last_processing>PDBe</last_processing>
        </sites>
        <key_dates>
            <deposition>2015-05-07</deposition>
            <header_release>2015-06-17</header_release>
            <obsolete>2015-12-16</obsolete>
            <update>2016-05-11</update>
        </key_dates>
        <superseded_by_list>
            <entry>
                <entry>EMD-3283</entry>
            </entry>
        </superseded_by_list>
        <title>The Structure of Human BK Polyomavirus at 6.5 A resolution</title>
        <authors_list>
            <author>Hurdiss D</author>
            <author>Thompson R</author>
            <author>Prescott EL</author>
            <author>Panou M</author>
            <author>Macdonald A</author>
            <author>Ranson NA</author>
        </authors_list>
        <keywords>BK Polyomavirus, BKPyV, BKV</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="false">
                    <author order="1">Hurdiss D</author>
                    <author order="2">Thompson R</author>
                    <author order="3">Prescott EL</author>
                    <author order="4">Panou M</author>
                    <author order="5">Macdonald A</author>
                    <author order="6">Ranson NA</author>
                    <title>The Structure of Human BK Polyomavirus at 6.5 A resolution</title>
                    <journal>To Be Published</journal>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>BK Polyomavirus</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>BK Polyomavirus</name>
                <oligomeric_state>Icosohedral</oligomeric_state>
                <number_unique_components>1</number_unique_components>
            </sample_supramolecule>
            <virus_supramolecule supramolecule_id="1">
                <name>BK polyomavirus</name>
                <sci_species_name ncbi="10629">BK polyomavirus</sci_species_name>
                <sci_species_strain>Dunlop</sci_species_strain>
                <natural_host database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                    <synonym_organism>VERTEBRATES</synonym_organism>
                </natural_host>
                <host_system database="NCBI">
                    <recombinant_organism ncbi="9534">Chlorocebus aethiops</recombinant_organism>
                    <recombinant_cell>Vero</recombinant_cell>
                </host_system>
                <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">
                    <buffer>
                        <ph>7.4</ph>
                        <details>10mM HEPES pH 7.9, 1mM CaCl2, 1mM MgCl2, 5mM KCl</details>
                    </buffer>
                    <grid>
                        <details>Quantifoil R2/1 EM grids</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">100</chamber_humidity>
                        <instrument>FEI VITROBOT MARK IV</instrument>
                        <method>6.5 seconds blot before plunging</method>
                    </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</nominal_cs>
                    <nominal_defocus_min units="µm">0.6</nominal_defocus_min>
                    <nominal_defocus_max units="µm">4.8</nominal_defocus_max>
                    <nominal_magnification>19000.0</nominal_magnification>
                    <specimen_holder_model>GATAN LIQUID NITROGEN</specimen_holder_model>
                    <date>2014-12-12</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">GATAN K2 (4k x 4k)</film_or_detector_model>
                            <number_real_images>432</number_real_images>
                            <average_electron_dose_per_image units="e/Å^2">40</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                    <specimen_holder>626b</specimen_holder>
                    <tilt_angle_min>0</tilt_angle_min>
                    <tilt_angle_max>0</tilt_angle_max>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <ctf_correction>
                    <details>CTFFIND3</details>
                </ctf_correction>
                <final_reconstruction>
                    <resolution units="Å" res_type="BY AUTHOR">6.55</resolution>
                    <resolution_method>OTHER</resolution_method>
                    <software_list>
                        <software>
                            <name>Relion</name>
                        </software>
                    </software_list>
                    <number_images_used>3394</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="221185">
        <file>emd_3000.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>384</col>
            <row>384</row>
            <sec>384</sec>
        </dimensions>
        <origin>
            <col>-192</col>
            <row>-192</row>
            <sec>-192</sec>
        </origin>
        <spacing>
            <x>384</x>
            <y>384</y>
            <z>384</z>
        </spacing>
        <cell>
            <a units="Å">691.19995</a>
            <b units="Å">691.19995</b>
            <c units="Å">691.19995</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>-0.02679493</minimum>
            <maximum>0.07481748</maximum>
            <average>0.00121312</average>
            <std>0.00959812</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">1.7999998</x>
            <y units="Å">1.7999998</y>
            <z units="Å">1.7999998</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.025</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Reconstruction of BK polyomavirus (sharpened map)</annotation_details>
        <details>::::EMDATABANK.org::::EMD-3000::::</details>
    </map>
    <validation>
        <fsc_curve>
            <file>emd_3000_fsc.xml</file>
        </fsc_curve>
    </validation>
</emd>
