<emd emdb_id="EMD-5534" 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>2012-12-04</deposition>
            <header_release>2013-07-03</header_release>
            <map_release>2013-09-04</map_release>
            <update>2013-09-25</update>
        </key_dates>
        <title>Visualization of Bacteriophage T7 Infection by Cryo-Electron Tomography</title>
        <authors_list>
            <author>Hu B</author>
            <author>Margolin W</author>
            <author>Molineux IJ</author>
            <author>Liu J</author>
        </authors_list>
        <keywords>Bacteriophage infection E. coli minicell DNA ejection</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Hu B</author>
                    <author order="2">Margolin W</author>
                    <author order="3">Molineux IJ</author>
                    <author order="4">Liu J</author>
                    <title>The bacteriophage t7 virion undergoes extensive structural remodeling during infection.</title>
                    <journal>SCIENCE</journal>
                    <volume>339</volume>
                    <first_page>576</first_page>
                    <last_page>579</last_page>
                    <year>2013</year>
                    <external_references type="PUBMED">23306440</external_references>
                    <external_references type="DOI">doi:10.1126/science.1231887</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-5535</emdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-5536</emdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-5537</emdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </emdb_reference>
        </emdb_list>
    </crossreferences>
    <sample>
        <name>Bacteriophage T7 infecting E. coli cell</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Bacteriophage T7 infecting E. coli cell</name>
                <number_unique_components>2</number_unique_components>
            </sample_supramolecule>
            <virus_supramolecule supramolecule_id="1">
                <name synonym="Bacteriophage T7">Enterobacteria phage T7</name>
                <sci_species_name ncbi="10760">Enterobacteria phage T7</sci_species_name>
                <natural_host database="NCBI">
                    <organism ncbi="562">Escherichia coli</organism>
                    <synonym_organism>BACTERIA(EUBACTERIA)</synonym_organism>
                </natural_host>
                <host_system database="NCBI" />
                <virus_shell shell_id="1">
                    <name>capsid</name>
                    <diameter units="&#8491;">600</diameter>
                </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>Bacteriophage T7</syn_species_name>
            </virus_supramolecule>
            <organelle_or_cellular_component_supramolecule supramolecule_id="2">
                <name>Bacteriophage infection</name>
                <recombinant_exp_flag>false</recombinant_exp_flag>
                <natural_source database="NCBI">
                    <organism ncbi="562">Escherichia coli</organism>
                </natural_source>
                <recombinant_expression database="NCBI" />
            </organelle_or_cellular_component_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>7.8</ph>
                        <details>50 mM Tris-HCl, 10 mM MgCl2, 0.1 M NaCl</details>
                    </buffer>
                    <grid>
                        <details>200 mesh grid</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_temperature units="K">100</chamber_temperature>
                        <instrument>HOMEMADE PLUNGER</instrument>
                        <method>Blot for 3 seconds before plunging.</method>
                    </vitrification>
                </subtomogram_averaging_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <subtomogram_averaging_microscopy microscopy_id="1">
                    <microscope>FEI POLARA 300</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_defocus_min units="&#181;m">4.0</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">6.0</nominal_defocus_max>
                    <nominal_magnification>31000.0</nominal_magnification>
                    <specimen_holder_model>GATAN LIQUID NITROGEN</specimen_holder_model>
                    <temperature>
                        <temperature_min units="K">90</temperature_min>
                        <temperature_max units="K">100</temperature_max>
                        <temperature_average units="K">95</temperature_average>
                    </temperature>
                    <alignment_procedure>
                        <legacy>
                            <astigmatism>Objective lens astigmatism was corrected at 200,000x magnification</astigmatism>
                        </legacy>
                    </alignment_procedure>
                    <date>2011-03-16</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">GENERIC TVIPS (4k x 4k)</film_or_detector_model>
                            <average_electron_dose_per_image units="e/&#8491;^2">100</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                    <specimen_holder>Liquid Nitrogen cooled</specimen_holder>
                    <tilt_series>
                        <axis1>
                            <min_angle units="deg">-64</min_angle>
                            <max_angle units="deg">64</max_angle>
                        </axis1>
                    </tilt_series>
                </subtomogram_averaging_microscopy>
            </microscopy_list>
            <subtomogram_averaging_processing image_processing_id="1">
                <details>The particles were manually selected from cryo-tomograms.</details>
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">40.0</resolution>
                    <resolution_method>OTHER</resolution_method>
                    <software_list>
                        <software>
                            <name>IMOD, Raptor, Protomo</name>
                        </software>
                    </software_list>
                    <number_subtomograms_used>1886</number_subtomograms_used>
                </final_reconstruction>
                <ctf_correction>
                    <details>No CTF correction</details>
                </ctf_correction>
                <final_three_d_classification>
                    <number_classes>4</number_classes>
                </final_three_d_classification>
            </subtomogram_averaging_processing>
        </structure_determination>
    </structure_determination_list>
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        <file>emd_5534.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>136</col>
            <row>136</row>
            <sec>256</sec>
        </dimensions>
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            <col>-68</col>
            <row>-68</row>
            <sec>-128</sec>
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        <spacing>
            <x>136</x>
            <y>136</y>
            <z>256</z>
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        <cell>
            <a units="&#8491;">775.19995</a>
            <b units="&#8491;">775.19995</b>
            <c units="&#8491;">1459.2</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>-4.47909164</minimum>
            <maximum>5.22529221</maximum>
            <average>-0.00000001</average>
            <std>1.0</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">5.7</x>
            <y units="&#8491;">5.7</y>
            <z units="&#8491;">5.7</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.25</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Asymmetrical reconstruction of bacteriophage T7 infecting E. coli with a trans-membrane channel.</annotation_details>
        <details>::::EMDATABANK.org::::EMD-5534::::</details>
    </map>
</emd>