<emd emdb_id="EMD-5717" 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>2013-07-11</deposition>
            <header_release>2013-08-21</header_release>
            <map_release>2014-04-23</map_release>
            <update>2014-04-30</update>
        </key_dates>
        <title>The structure of Sinorhizobium meliloti phage phiM12, a novel T=19 icosahedral phage that is the founder of a new group of T4-like phages</title>
        <authors_list>
            <author>Stroupe ME</author>
            <author>Brewer TE</author>
            <author>Sousa DR</author>
            <author>Jones KM</author>
        </authors_list>
        <keywords>bacteriophage, phiM12, Sinorhizobium meliloti, T=19, rhizobia</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Stroupe ME</author>
                    <author order="2">Brewer TE</author>
                    <author order="3">Sousa DR</author>
                    <author order="4">Jones KM</author>
                    <title>The structure of Sinorhizobium meliloti phage phiM12, which has a novel T=19l triangulation number and is the founder of a new group of T4-superfamily phages.</title>
                    <journal>VIROLOGY</journal>
                    <volume>450</volume>
                    <first_page>205</first_page>
                    <last_page>212</last_page>
                    <year>2014</year>
                    <external_references type="PUBMED">24503083</external_references>
                    <external_references type="DOI">doi:10.1016/j.virol.2013.11.019</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-5718</emdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </emdb_reference>
        </emdb_list>
    </crossreferences>
    <sample>
        <name>T=19 icosahedral shell packed with DNA from phiM12, a bacteriophage of Sinorhizobium meliloti</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>T=19 icosahedral shell packed with DNA from phiM12, a bacteriophage of Sinorhizobium meliloti</name>
                <oligomeric_state>icosahedral</oligomeric_state>
                <number_unique_components>2</number_unique_components>
            </sample_supramolecule>
            <virus_supramolecule supramolecule_id="1">
                <name>Sinorhizobium phage phiM12</name>
                <sci_species_name ncbi="1357423">Sinorhizobium phage phiM12</sci_species_name>
                <sci_species_strain>phiM12</sci_species_strain>
                <natural_host database="NCBI">
                    <organism ncbi="382">Sinorhizobium meliloti</organism>
                    <strain>1021</strain>
                    <synonym_organism>BACTERIA(EUBACTERIA)</synonym_organism>
                </natural_host>
                <host_system database="NCBI" />
                <virus_shell shell_id="1">
                    <name>1</name>
                    <diameter units="&#8491;">1000</diameter>
                    <triangulation>19</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>singleParticle</method>
            <aggregation_state>particle</aggregation_state>
            <specimen_preparation_list>
                <single_particle_preparation preparation_id="1">
                    <buffer>
                        <ph>7.0</ph>
                        <details>10 mM Na2HPO4, 1 mM MgSO4</details>
                    </buffer>
                    <grid>
                        <details>200 mesh 2/2 Quantifoil</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">100</chamber_humidity>
                        <chamber_temperature units="K">120</chamber_temperature>
                        <instrument>FEI VITROBOT MARK IV</instrument>
                        <method>blot 4 seconds</method>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>FEI TITAN KRIOS</microscope>
                    <illumination_mode>FLOOD BEAM</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>FIELD EMISSION GUN</electron_source>
                    <acceleration_voltage units="kV">120</acceleration_voltage>
                    <nominal_defocus_min units="&#181;m">1.5</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">3.5</nominal_defocus_max>
                    <nominal_magnification>59000.0</nominal_magnification>
                    <calibrated_magnification>65555.0</calibrated_magnification>
                    <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
                    <date>2013-05-13</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">GATAN ULTRASCAN 4000 (4k x 4k)</film_or_detector_model>
                            <number_real_images>1000</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">15</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                    <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">
                <details>Images were selected by hand; initial model determined in EMAN and refined in EMAN and Frealign.</details>
                <ctf_correction>
                    <details>micrograph</details>
                </ctf_correction>
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">13.0</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>EMAN, FREALIGN</name>
                        </software>
                    </software_list>
                    <number_images_used>2038</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="43905">
        <file>emd_5717.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>224</col>
            <row>224</row>
            <sec>224</sec>
        </dimensions>
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            <col>0</col>
            <row>0</row>
            <sec>0</sec>
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            <x>224</x>
            <y>224</y>
            <z>224</z>
        </spacing>
        <cell>
            <a units="&#8491;">1209.6</a>
            <b units="&#8491;">1209.6</b>
            <c units="&#8491;">1209.6</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>-0.06335218</minimum>
            <maximum>0.28843483</maximum>
            <average>0.04192379</average>
            <std>0.09811363</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">5.4</x>
            <y units="&#8491;">5.4</y>
            <z units="&#8491;">5.4</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.1</level>
                <source>EMDB</source>
            </contour>
        </contour_list>
        <annotation_details>Cryo-EM reconstruction of phiM12, packed with DNA</annotation_details>
        <details>::::EMDATABANK.org::::EMD-5717::::</details>
    </map>
</emd>