<?xml version='1.0' encoding='utf-8'?>
<emd emdb_id="EMD-9392" version="3.0.1.3" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="https://github.com/emdb-empiar/emdb-schemas/blob/master/v3/v3_0_1_3/emdb.xsd">
    <admin>
        <current_status>
            <date>2019-03-27</date>
            <code>REL</code>
            <processing_site>RCSB</processing_site>
        </current_status>
        <sites>
            <deposition>RCSB</deposition>
            <last_processing>RCSB</last_processing>
        </sites>
        <key_dates>
            <deposition>2019-01-04</deposition>
            <header_release>2018-05-02</header_release>
            <map_release>2019-03-27</map_release>
            <update>2019-03-27</update>
        </key_dates>
        <title>Bacteriophage L virion</title>
        <authors_list>
            <author>Parent KN</author>
            <author>Schrad JR</author>
        </authors_list>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="false">
                    <author order="1">Parent KN</author>
                    <title>Bacteriophage L Dec protein</title>
                    <journal_abbreviation>To Be Published</journal_abbreviation>
                    <external_references type="CSD">0353</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-9392</emdb_id>
                <relationship>
                    <other>associated EM volume</other>
                </relationship>
            </emdb_reference>
        </emdb_list>
    </crossreferences>
    <sample>
        <name>Enterobacteria phage L</name>
        <supramolecule_list>
            <virus_supramolecule supramolecule_id="1">
                <name>Enterobacteria phage L</name>
                <parent>0</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>1</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <sci_species_name ncbi="45441">Enterobacteria phage L</sci_species_name>
                <natural_host database="NCBI">
                    <organism ncbi="90371">Salmonella enterica subsp. enterica serovar Typhimurium</organism>
                </natural_host>
                <molecular_weight>
                    <theoretical units="MDa">60</theoretical>
                </molecular_weight>
                <virus_shell shell_id="1">
                    <name>coat protein</name>
                    <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>singleParticle</method>
            <aggregation_state>particle</aggregation_state>
            <specimen_preparation_list>
                <single_particle_preparation preparation_id="1">
                    <concentration units="mg/mL">1</concentration>
                    <buffer>
                        <ph>7.6</ph>
                        <component>
                            <concentration units="mM">10.0</concentration>
                            <formula>MgCl2</formula>
                            <name>magnesium chloride</name>
                        </component>
                        <component>
                            <concentration units="mM">10.0</concentration>
                            <formula>C4H11NO3</formula>
                            <name>Tris</name>
                        </component>
                    </buffer>
                    <grid>
                        <support_film film_type_id="1">
                            <film_material>CARBON</film_material>
                            <film_topology>HOLEY</film_topology>
                            <film_thickness units="nm">100.0</film_thickness>
                        </support_film>
                        <details>unspecified</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <instrument>HOMEMADE PLUNGER</instrument>
                        <details />
                    </vitrification>
                    <details>concentration is 1x10^12 phage/mL</details>
                </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">300</acceleration_voltage>
                    <nominal_cs units="mm">2.7</nominal_cs>
                    <nominal_defocus_min units="µm">0.35</nominal_defocus_min>
                    <nominal_defocus_max units="µm">2.49</nominal_defocus_max>
                    <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
                    <cooling_holder_cryogen>NITROGEN</cooling_holder_cryogen>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>DIRECT ELECTRON DE-20 (5k x 3k)</film_or_detector_model>
                            <detector_mode>INTEGRATING</detector_mode>
                            <digitization_details>
                                <dimensions>
                                    <width units="pixel">5000</width>
                                    <height units="pixel">4000</height>
                                </dimensions>
                                <sampling_interval units="µm">6.4</sampling_interval>
                                <frames_per_image>0-53</frames_per_image>
                            </digitization_details>
                            <number_grids_imaged>1</number_grids_imaged>
                            <number_real_images>494</number_real_images>
                            <average_exposure_time units="s">2.0</average_exposure_time>
                            <average_electron_dose_per_image units="e/Å^2">27.0</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <image_recording_id>1</image_recording_id>
                <details>images were motion corrected and also particles were corrected for damage compensation</details>
                <ctf_correction>
                    <software_list>
                        <software>
                            <name>Auto3DEM</name>
                            <version>v4.01.07</version>
                        </software>
                    </software_list>
                    <details>estimated manually</details>
                </ctf_correction>
                <startup_model type_of_model="OTHER">
                    <details>random model computation</details>
                </startup_model>
                <final_reconstruction>
                    <applied_symmetry>
                        <point_group>I</point_group>
                    </applied_symmetry>
                    <resolution res_type="BY AUTHOR" units="Å">4.2</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>Auto3DEM</name>
                            <version>v4.01.07</version>
                        </software>
                    </software_list>
                    <number_images_used>7879</number_images_used>
                </final_reconstruction>
                <initial_angle_assignment>
                    <type>PROJECTION MATCHING</type>
                    <projection_matching_processing />
                    <software_list>
                        <software>
                            <name>Auto3DEM</name>
                            <version>v4.01.07</version>
                        </software>
                    </software_list>
                </initial_angle_assignment>
                <final_angle_assignment>
                    <type>PROJECTION MATCHING</type>
                    <projection_matching_processing />
                    <software_list>
                        <software>
                            <name>Auto3DEM</name>
                            <version>v4.01.07</version>
                        </software>
                    </software_list>
                </final_angle_assignment>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="80495">
        <file>emd_9392.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>272</col>
            <row>272</row>
            <sec>272</sec>
        </dimensions>
        <origin>
            <col>-136</col>
            <row>-136</row>
            <sec>-136</sec>
        </origin>
        <spacing>
            <x>272</x>
            <y>272</y>
            <z>272</z>
        </spacing>
        <cell>
            <a units="Å">342.72</a>
            <b units="Å">342.72</b>
            <c units="Å">342.72</c>
            <alpha units="deg">90.0</alpha>
            <beta units="deg">90.0</beta>
            <gamma units="deg">90.0</gamma>
        </cell>
        <axis_order>
            <fast>Z</fast>
            <medium>Y</medium>
            <slow>X</slow>
        </axis_order>
        <statistics>
            <minimum>-8.963733</minimum>
            <maximum>17.443864999999999</maximum>
            <average>0.000000000000033</average>
            <std>1.0</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">1.26</x>
            <y units="Å">1.26</y>
            <z units="Å">1.26</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>2.18</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-9392::::</label>
        <annotation_details>1/8th of the virion for phage L-segmentation shows capsid protein only</annotation_details>
    </map>
    <interpretation>
        <additional_map_list>
            <additional_map format="CCP4" size_kbytes="768">
                <file>emd_9392_additional.map.gz</file>
                <symmetry>
                    <space_group>1</space_group>
                </symmetry>
                <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
                <dimensions>
                    <col>58</col>
                    <row>57</row>
                    <sec>58</sec>
                </dimensions>
                <origin>
                    <col>-29</col>
                    <row>-28</row>
                    <sec>-29</sec>
                </origin>
                <spacing>
                    <x>58</x>
                    <y>57</y>
                    <z>58</z>
                </spacing>
                <cell>
                    <a units="Å">73.08</a>
                    <b units="Å">71.82</b>
                    <c units="Å">73.08</c>
                    <alpha units="deg">90.0</alpha>
                    <beta units="deg">90.0</beta>
                    <gamma units="deg">90.0</gamma>
                </cell>
                <axis_order>
                    <fast>Z</fast>
                    <medium>Y</medium>
                    <slow>X</slow>
                </axis_order>
                <statistics>
                    <minimum>-5.053801</minimum>
                    <maximum>10.253301</maximum>
                    <average>-0.000000000017204</average>
                    <std>1.0</std>
                </statistics>
                <pixel_spacing>
                    <x units="Å">1.26</x>
                    <y units="Å">1.26</y>
                    <z units="Å">1.26</z>
                </pixel_spacing>
                <contour_list>
                    <contour primary="true">
                        <source>AUTHOR</source>
                    </contour>
                </contour_list>
                <label>::::EMDATABANK.org::::EMD-9392::::</label>
                <annotation_details>single Dec trimer segmented from phage L virion map</annotation_details>
            </additional_map>
        </additional_map_list>
    </interpretation>
</emd>