<emd emdb_id="EMD-6043" 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>2014-08-20</deposition>
            <header_release>2014-09-24</header_release>
            <map_release>2014-09-24</map_release>
            <update>2016-02-17</update>
        </key_dates>
        <title>Structure of the Head of Bacteriophage Basilisk to 18 Angstrom resolution</title>
        <authors_list>
            <author>Grose JH</author>
            <author>Belnap DM</author>
            <author>Jensen JD</author>
            <author>Mathis AD</author>
            <author>Prince JT</author>
            <author>Merrill B</author>
            <author>Burnett SH</author>
            <author>Breakwell DP</author>
        </authors_list>
        <keywords>bacteriophage, icosahedron, triangulation number, T=9, capsid, siphovirus, HK97 fold, Bacillus cereus</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Grose JH</author>
                    <author order="2">Belnap DM</author>
                    <author order="3">Jensen JD</author>
                    <author order="4">Mathis AD</author>
                    <author order="5">Prince JT</author>
                    <author order="6">Merrill B</author>
                    <author order="7">Burnett SH</author>
                    <author order="8">Breakwell DP</author>
                    <title>The Genomes, Proteomes and Structure of Three Novel Phages that Infect the Bacillus Cereus Group and Carry Putative Virulence Factors.</title>
                    <journal>J.VIROL.</journal>
                    <volume>88</volume>
                    <first_page>11846</first_page>
                    <last_page>11860</last_page>
                    <year>2014</year>
                    <external_references type="PUBMED">25100842</external_references>
                    <external_references type="DOI">doi:10.1128/JVI.01364-14</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>Bacteriophage Basilisk Head</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Bacteriophage Basilisk Head</name>
                <oligomeric_state>icosahedral</oligomeric_state>
                <number_unique_components>1</number_unique_components>
            </sample_supramolecule>
            <virus_supramolecule supramolecule_id="1">
                <name synonym="Bacteriophage Basilisk, Basilisk Phage">Bacillus phage Basilisk</name>
                <details>Bacteriophage Basilisk head component (NCBI taxonomy ID 1296654)</details>
                <sci_species_name>Bacillus phage Basilisk</sci_species_name>
                <natural_host database="NCBI">
                    <organism ncbi="1396">Bacillus cereus</organism>
                    <strain>BC7003</strain>
                    <synonym_organism>BACTERIA(EUBACTERIA)</synonym_organism>
                </natural_host>
                <host_system database="NCBI" />
                <virus_shell shell_id="1">
                    <name>capsid</name>
                    <diameter units="&#8491;">780</diameter>
                    <triangulation>9</triangulation>
                </virus_shell>
                <virus_type>VIRION</virus_type>
                <virus_isolate>SPECIES</virus_isolate>
                <virus_enveloped>false</virus_enveloped>
                <virus_empty>false</virus_empty>
                <syn_species_name>Bacteriophage Basilisk, Basilisk Phage</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>
                        <details>PBS (phosphate-buffered saline)</details>
                    </buffer>
                    <staining>
                        <type>NEGATIVE</type>
                        <details>no stain used</details>
                    </staining>
                    <grid>
                        <details>holey carbon film (randomly sized holes) on copper grid</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <instrument>FEI VITROBOT MARK II</instrument>
                        <details>Blotting chamber (and sample) was maintained at 4 degrees Celsius before plunging; sample was applied with cold pipette tips. Humidity was 81-89%.</details>
                        <method>blotted 1-2 seconds 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">2.0</nominal_cs>
                    <nominal_defocus_min units="&#181;m">0.0</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">3.3</nominal_defocus_max>
                    <nominal_magnification>29000.0</nominal_magnification>
                    <calibrated_magnification>31400.0</calibrated_magnification>
                    <specimen_holder_model>GATAN LIQUID NITROGEN</specimen_holder_model>
                    <date>2014-02-14</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="FILM">KODAK SO-163 FILM</film_or_detector_model>
                            <digitization_details>
                                <scanner>NIKON SUPER COOLSCAN 9000</scanner>
                                <sampling_interval units="&#181;m">6.35</sampling_interval>
                            </digitization_details>
                            <number_real_images>20</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">4.4</average_electron_dose_per_image>
                            <details>16-bit scanned images truncated to 8-bit</details>
                            <bits_per_pixel>16.</bits_per_pixel>
                        </image_recording>
                    </image_recording_list>
                    <specimen_holder>nitrogen cooled</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">
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">18.0</resolution>
                    <resolution_method>OTHER</resolution_method>
                    <software_list>
                        <software>
                            <name>AUTO3DEM</name>
                        </software>
                    </software_list>
                    <number_images_used>2085</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="143673">
        <file>emd_6043.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS SIGNED INTEGER (2 BYTES)</data_type>
        <dimensions>
            <col>419</col>
            <row>419</row>
            <sec>419</sec>
        </dimensions>
        <origin>
            <col>-209</col>
            <row>-209</row>
            <sec>-209</sec>
        </origin>
        <spacing>
            <x>419</x>
            <y>419</y>
            <z>419</z>
        </spacing>
        <cell>
            <a units="&#8491;">846.38</a>
            <b units="&#8491;">846.38</b>
            <c units="&#8491;">846.38</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>-13407.0</minimum>
            <maximum>32443.0</maximum>
            <average>2373.525634770000124</average>
            <std>4594.930175780000354</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">2.02</x>
            <y units="&#8491;">2.02</y>
            <z units="&#8491;">2.02</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>4150.0</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Reconstruction of Basilisk Bacteriophage Head</annotation_details>
        <details>::::EMDATABANK.org::::EMD-6043::::</details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <initial_model>
                    <access_code>1OHG</access_code>
                </initial_model>
                <refinement_protocol>RIGID BODY FIT</refinement_protocol>
                <refinement_space>REAL</refinement_space>
            </modelling>
        </modelling_list>
        <figure_list>
            <figure>
                <file>emd_6043.tif</file>
            </figure>
        </figure_list>
    </interpretation>
</emd>