<emd emdb_id="EMD-6398" 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>2015-07-23</deposition>
            <header_release>2015-08-12</header_release>
            <map_release>2016-07-27</map_release>
            <update>2016-07-27</update>
        </key_dates>
        <title>Electron cryo-microscopy of a Propionibacterium acnes phage</title>
        <authors_list>
            <author>Chiou J</author>
            <author>Zhang X</author>
            <author>Marinelli LJ</author>
            <author>Modlin RL</author>
            <author>Zhou ZH</author>
        </authors_list>
        <keywords>acne, bacteriophage, cryoEM, HK97-like</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="false">
                    <author order="1">Chiou J</author>
                    <author order="2">Zhang X</author>
                    <author order="3">Marinelli LJ</author>
                    <author order="4">Modlin RL</author>
                    <author order="5">Zhou ZH</author>
                    <title>Capsid Structure of the Propionibacterium acnes Bacteriophage ATCC_Clear</title>
                    <journal>To Be Published</journal>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>3jb5</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>Propionibacterium acnes bacteriophage ATCC_Clear capsid structure</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Propionibacterium acnes bacteriophage ATCC_Clear capsid structure</name>
                <number_unique_components>1</number_unique_components>
                <molecular_weight>
                    <experimental units="MDa">33</experimental>
                    <method>SDS-PAGE/MS</method>
                </molecular_weight>
            </sample_supramolecule>
            <virus_supramolecule supramolecule_id="1">
                <name synonym="Propionibacterium acnes bacteriophage">Propionibacterium phage PA6</name>
                <details>Mature virions, DNA inside masked</details>
                <sci_species_name ncbi="376758">Propionibacterium phage PA6</sci_species_name>
                <sci_species_strain>ATCC 29399B_C</sci_species_strain>
                <natural_host database="NCBI">
                    <organism ncbi="1747">Propionibacterium acnes</organism>
                    <strain>6919</strain>
                    <synonym_organism>BACTERIA(EUBACTERIA)</synonym_organism>
                </natural_host>
                <host_system database="NCBI" />
                <virus_shell shell_id="1">
                    <diameter units="&#8491;">660</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>
                <syn_species_name>Propionibacterium acnes bacteriophage</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">
                    <grid>
                        <details>Purified sample was applied to a Quantifoil grid</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">100</chamber_humidity>
                        <instrument>FEI VITROBOT MARK IV</instrument>
                        <method>Blot for 15 seconds before plunging</method>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>FEI TITAN KRIOS</microscope>
                    <illumination_mode>SPOT SCAN</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">0.8</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">2.27</nominal_defocus_max>
                    <nominal_magnification>38462.0</nominal_magnification>
                    <calibrated_magnification>38462.0</calibrated_magnification>
                    <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
                    <date>2014-05-16</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">GATAN K2 (4k x 4k)</film_or_detector_model>
                            <number_real_images>3168</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">25</average_electron_dose_per_image>
                            <details>Every image is the average of twelve frames recorded by the direct electron detector.</details>
                        </image_recording>
                    </image_recording_list>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <details>The particles were selected using an in-house selection procedure.</details>
                <final_reconstruction>
                    <resolution res_type="BY AUTHOR" units="&#8491;">3.7</resolution>
                    <resolution_method>OTHER</resolution_method>
                    <software_list>
                        <software>
                            <name>FREALIGN</name>
                        </software>
                    </software_list>
                    <number_images_used>27504</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="549251">
        <file>emd_6398.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>520</col>
            <row>520</row>
            <sec>520</sec>
        </dimensions>
        <origin>
            <col>-260</col>
            <row>-260</row>
            <sec>-260</sec>
        </origin>
        <spacing>
            <x>520</x>
            <y>520</y>
            <z>520</z>
        </spacing>
        <cell>
            <a units="&#8491;">676.0</a>
            <b units="&#8491;">676.0</b>
            <c units="&#8491;">676.0</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>-0.18350838</minimum>
            <maximum>0.23970643</maximum>
            <average>-0.00263189</average>
            <std>0.01325464</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">1.3</x>
            <y units="&#8491;">1.3</y>
            <z units="&#8491;">1.3</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.0625</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Reconstruction of Propionibacterium acnes phage</annotation_details>
        <details>::::EMDATABANK.org::::EMD-6398::::</details>
    </map>
    <interpretation>
        <figure_list>
            <figure>
                <file>emd_6398.jpg</file>
            </figure>
        </figure_list>
    </interpretation>
</emd>