<emd emdb_id="EMD-6427" 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>PDBj</processing_site>
        </current_status>
        <sites>
            <deposition>RCSB</deposition>
            <last_processing>PDBj</last_processing>
        </sites>
        <key_dates>
            <deposition>2015-08-15</deposition>
            <header_release>2015-11-18</header_release>
            <map_release>2016-10-26</map_release>
            <update>2016-10-26</update>
        </key_dates>
        <title>Visualizing the Adsorption of Cyanophage P-SSP7 to the Marine Cyanobacterium Prochlorococcus MED4 by Electron Cryo-Tomography</title>
        <authors_list>
            <author>Murata K</author>
            <author>Zhang Q</author>
            <author>Fu C</author>
            <author>Liu X</author>
            <author>Sullivan M</author>
            <author>Coleman M</author>
            <author>Osburne M</author>
            <author>Schmid MF</author>
            <author>Chisholm S</author>
            <author>Chiu W</author>
        </authors_list>
        <keywords>cryo-electron tomography, bacteriophage, cyanobacteria</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="false">
                    <author order="1">Murata K</author>
                    <author order="2">Zhang Q</author>
                    <author order="3">Fu C</author>
                    <author order="4">Liu X</author>
                    <author order="5">Sullivan M</author>
                    <author order="6">Coleman M</author>
                    <author order="7">Osburne M</author>
                    <author order="8">Schmid MF</author>
                    <author order="9">Chisholm S</author>
                    <author order="10">Chiu W</author>
                    <title>Visualizing the Adsorption of Cyanophage P-SSP7 to the Marine Cyanobacterium Prochlorococcus MED4 by Electron Cryo-Tomography</title>
                    <journal>J.MOL.BIOL.</journal>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>Prochlorococcus phage P-SSP7</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Prochlorococcus phage P-SSP7</name>
                <number_unique_components>1</number_unique_components>
            </sample_supramolecule>
            <virus_supramolecule supramolecule_id="1">
                <name>Prochlorococcus phage P-SSP7</name>
                <sci_species_name ncbi="268748">Prochlorococcus phage P-SSP7</sci_species_name>
                <sci_species_strain>Podoviridae</sci_species_strain>
                <natural_host database="NCBI">
                    <organism ncbi="1218">Prochlorococcus</organism>
                    <strain>MED4</strain>
                    <synonym_organism>BACTERIA(EUBACTERIA)</synonym_organism>
                </natural_host>
                <host_system database="NCBI" />
                <virus_shell shell_id="1">
                    <diameter units="&#8491;">655</diameter>
                    <triangulation>7</triangulation>
                </virus_shell>
                <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>subtomogramAveraging</method>
            <aggregation_state>particle</aggregation_state>
            <specimen_preparation_list>
                <subtomogram_averaging_preparation preparation_id="1">
                    <buffer>
                        <ph>7.5</ph>
                        <details>100 mM Tris-HCl (pH 7.5), 100 mM MgSO4, and 30 mM NaCl</details>
                    </buffer>
                    <grid>
                        <details>R3.5/1 Quantifoil</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">40</chamber_humidity>
                        <chamber_temperature units="K">120</chamber_temperature>
                        <instrument>LEICA EM CPC</instrument>
                        <method>Grids with sample solution were quickly frozen in liquid ethane.</method>
                    </vitrification>
                </subtomogram_averaging_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <subtomogram_averaging_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_cs units="mm">4.1</nominal_cs>
                    <nominal_defocus_min units="&#181;m">3.0</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">5.0</nominal_defocus_max>
                    <nominal_magnification>20000.0</nominal_magnification>
                    <specimen_holder_model>JEOL 3200FSC CRYOHOLDER</specimen_holder_model>
                    <temperature>
                        <temperature_average units="K">90</temperature_average>
                    </temperature>
                    <specialist_optics>
                        <energy_filter>
                            <name>Omega</name>
                            <lower_energy_threshold units="eV">0.0</lower_energy_threshold>
                            <upper_energy_threshold units="eV">30.0</upper_energy_threshold>
                        </energy_filter>
                    </specialist_optics>
                    <date>2008-05-16</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">GATAN ULTRASCAN 4000 (4k x 4k)</film_or_detector_model>
                            <average_electron_dose_per_image units="e/&#8491;^2">80</average_electron_dose_per_image>
                            <bits_per_pixel>16.</bits_per_pixel>
                        </image_recording>
                    </image_recording_list>
                    <tilt_series>
                        <axis1>
                            <min_angle units="deg">0</min_angle>
                            <max_angle units="deg">62</max_angle>
                        </axis1>
                    </tilt_series>
                </subtomogram_averaging_microscopy>
            </microscopy_list>
            <subtomogram_averaging_processing image_processing_id="1">
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <resolution_method>OTHER</resolution_method>
                    <number_subtomograms_used>70</number_subtomograms_used>
                </final_reconstruction>
            </subtomogram_averaging_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="22783">
        <file>emd_6427.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>180</col>
            <row>180</row>
            <sec>180</sec>
        </dimensions>
        <origin>
            <col>-90</col>
            <row>-90</row>
            <sec>-90</sec>
        </origin>
        <spacing>
            <x>180</x>
            <y>180</y>
            <z>180</z>
        </spacing>
        <cell>
            <a units="&#8491;">1684.7999</a>
            <b units="&#8491;">1684.7999</b>
            <c units="&#8491;">1684.7999</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>-10.439310069999999</minimum>
            <maximum>12.64997005</maximum>
            <average>0.00177581</average>
            <std>0.99988359</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">9.36</x>
            <y units="&#8491;">9.36</y>
            <z units="&#8491;">9.36</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>1.5</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>pre-infection conformation of P-SSP7 bacteriophage</annotation_details>
        <details>::::EMDATABANK.org::::EMD-6427::::</details>
    </map>
</emd>