<emd emdb_id="EMD-5382" 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>2012-01-10</deposition>
            <header_release>2012-01-12</header_release>
            <map_release>2012-01-12</map_release>
            <update>2012-03-14</update>
        </key_dates>
        <title>Marine Bacteriophage SIO-2 with T12 symmetry (Mature Capsid)</title>
        <authors_list>
            <author>Lander GC</author>
            <author>Baudoux AC</author>
            <author>Azam F</author>
            <author>Potter CS</author>
            <author>Carragher B</author>
            <author>Johnson JE</author>
        </authors_list>
        <keywords>Marine Bacteriophage, Phage, Virus, Decoration Proteins, Ig-like</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Lander GC</author>
                    <author order="2">Baudoux AC</author>
                    <author order="3">Azam F</author>
                    <author order="4">Potter CS</author>
                    <author order="5">Carragher B</author>
                    <author order="6">Johnson JE</author>
                    <title>Capsomer dynamics and stabilization in the T = 12 marine bacteriophage SIO-2 and its procapsid studied by CryoEM.</title>
                    <journal>STRUCTURE</journal>
                    <volume>20</volume>
                    <first_page>498</first_page>
                    <last_page>503</last_page>
                    <year>2012</year>
                    <external_references type="PUBMED">22405008</external_references>
                    <external_references type="DOI">doi:10.1016/j.str.2012.01.007</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>Marine Phage SIO-2</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Marine Phage SIO-2</name>
                <details>phage are tailed</details>
                <oligomeric_state>mature capsid</oligomeric_state>
                <number_unique_components>1</number_unique_components>
                <molecular_weight>
                    <experimental units="MDa">50</experimental>
                    <method>Sedimentation</method>
                </molecular_weight>
            </sample_supramolecule>
            <virus_supramolecule supramolecule_id="1">
                <name synonym="SIO-2">Vibrio phage SIO-2</name>
                <sci_species_name ncbi="700512">Vibrio phage SIO-2</sci_species_name>
                <natural_host database="NCBI">
                    <organism>Vibrio sp. SWAT-3</organism>
                    <synonym_organism>BACTERIA(EUBACTERIA)</synonym_organism>
                </natural_host>
                <host_system database="NCBI" />
                <virus_shell shell_id="1">
                    <name>gene84</name>
                    <diameter units="&#8491;">800</diameter>
                    <triangulation>12</triangulation>
                </virus_shell>
                <virus_type>VIRION</virus_type>
                <virus_isolate>STRAIN</virus_isolate>
                <virus_enveloped>false</virus_enveloped>
                <virus_empty>false</virus_empty>
                <syn_species_name>SIO-2</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>100 kDa-filtered autoclaved seawater</details>
                    </buffer>
                    <grid>
                        <details>200 mesh Cu grid</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">100</chamber_humidity>
                        <chamber_temperature units="K">78</chamber_temperature>
                        <instrument>OTHER</instrument>
                        <details>Vitrification instrument: Vitrobot</details>
                        <method>blot for 4 seconds before plunging</method>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>FEI TECNAI 20</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">1.8</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">3.0</nominal_defocus_max>
                    <nominal_magnification>80000.0</nominal_magnification>
                    <calibrated_magnification>80000.0</calibrated_magnification>
                    <specimen_holder_model>SIDE ENTRY, EUCENTRIC</specimen_holder_model>
                    <temperature>
                        <temperature_min units="K">78</temperature_min>
                        <temperature_max units="K">78</temperature_max>
                        <temperature_average units="K">78</temperature_average>
                    </temperature>
                    <alignment_procedure>
                        <legacy>
                            <astigmatism>objective lens astigmatism was corrected at 210K times magnification</astigmatism>
                        </legacy>
                    </alignment_procedure>
                    <details>Collected using Leginon software</details>
                    <date>2009-06-13</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">TVIPS TEMCAM-F415 (4k x 4k)</film_or_detector_model>
                            <digitization_details>
                                <sampling_interval units="&#181;m">0.975</sampling_interval>
                            </digitization_details>
                            <number_real_images>6628</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">30</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                    <specimen_holder>Gatan CT3500</specimen_holder>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <details>particles automatically selected and manually edited</details>
                <ctf_correction>
                    <details>whole micrograph</details>
                </ctf_correction>
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">8.5</resolution>
                    <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>EMAN and Frealign</name>
                        </software>
                    </software_list>
                    <number_images_used>20983</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="432001">
        <file>emd_5382.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>480</col>
            <row>480</row>
            <sec>480</sec>
        </dimensions>
        <origin>
            <col>80</col>
            <row>80</row>
            <sec>80</sec>
        </origin>
        <spacing>
            <x>480</x>
            <y>480</y>
            <z>480</z>
        </spacing>
        <cell>
            <a units="&#8491;">936.0</a>
            <b units="&#8491;">936.0</b>
            <c units="&#8491;">936.0</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>-9.506665229999999</minimum>
            <maximum>13.96425533</maximum>
            <average>0.04441358</average>
            <std>0.84027171</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">1.95</x>
            <y units="&#8491;">1.95</y>
            <z units="&#8491;">1.95</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>2.0</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Mature SIO-2 phage</annotation_details>
        <details>::::EMDATABANK.org::::EMD-5382::::</details>
    </map>
</emd>