<?xml version="1.0" encoding="UTF-8"?>
<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="https://github.com/emdb-empiar/emdb-schemas/blob/master/v3/v3_0_1_9/emdb.xsd" emdb_id="EMD-22331" version="3.0.1.9">
    <admin>
        <current_status>
            <date>2020-09-02</date>
            <code>REL</code>
            <processing_site>RCSB</processing_site>
        </current_status>
        <sites>
            <deposition>RCSB</deposition>
            <last_processing>RCSB</last_processing>
        </sites>
        <key_dates>
            <deposition>2020-07-20</deposition>
            <header_release>2020-09-02</header_release>
            <map_release>2020-09-02</map_release>
            <update>2020-09-02</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)</funding_body>
                <code>UA5GM126533</code>
                <country>United States</country>
            </grant_reference>
        </grant_support>
        <title>SPN3US phage empty capsid</title>
        <authors_list>
            <author>Heymann JB</author>
            <author>Wang B</author>
            <author>Newcomb WW</author>
            <author>Wu W</author>
            <author>Winkler DC</author>
            <author>Cheng N</author>
            <author>Reilly ER</author>
            <author>Hsia R-C</author>
            <author>Thomas JA</author>
            <author>Steven AC</author>
        </authors_list>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Heymann JB</author>
                    <author order="2">Wang B</author>
                    <author order="3">Newcomb WW</author>
                    <author order="4">Wu W</author>
                    <author order="5">Winkler DC</author>
                    <author order="6">Cheng N</author>
                    <author order="7">Reilly ER</author>
                    <author order="8">Hsia RC</author>
                    <author order="9">Thomas JA</author>
                    <author order="10">Steven AC</author>
                    <title>The Mottled Capsid of theSalmonellaGiant Phage SPN3US, a Likely Maturation Intermediate with a Novel Internal Shell.</title>
                    <journal_abbreviation>Viruses</journal_abbreviation>
                    <volume>12</volume>
                    <year>2020</year>
                    <external_references type="PUBMED">32825132</external_references>
                    <external_references type="DOI">doi:10.3390/v12090910</external_references>
                    <external_references type="ISSN">1999-4915</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-22332</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-22333</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-22331</emdb_id>
                <relationship>
                    <other>associated EM volume</other>
                </relationship>
            </emdb_reference>
        </emdb_list>
    </crossreferences>
    <sample>
        <name>Salmonella phage SPN3US</name>
        <supramolecule_list>
            <virus_supramolecule supramolecule_id="1">
                <name>Salmonella phage SPN3US</name>
                <parent>0</parent>
                <sci_species_name ncbi="1090134">Salmonella phage SPN3US</sci_species_name>
                <natural_host database="NCBI">
                    <organism ncbi="28901">Salmonella enterica</organism>
                </natural_host>
                <host_system database="NCBI">
                    <recombinant_organism ncbi="28901">Salmonella enterica</recombinant_organism>
                    <recombinant_strain>Typhimurium T9079</recombinant_strain>
                </host_system>
                <molecular_weight>
                    <theoretical units="MDa">195</theoretical>
                </molecular_weight>
                <virus_shell shell_id="1">
                    <name>Capsid</name>
                    <diameter units="Å">1460.0</diameter>
                    <triangulation>27</triangulation>
                </virus_shell>
                <virus_type>VIRUS-LIKE PARTICLE</virus_type>
                <virus_isolate>OTHER</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">2</concentration>
                    <buffer>
                        <ph>8</ph>
                    </buffer>
                    <grid>
                        <model>Homemade</model>
                        <material>COPPER</material>
                        <support_film film_type_id="1">
                            <film_material>CARBON</film_material>
                            <film_topology>LACEY</film_topology>
                        </support_film>
                        <details>Grids were from Ted Pella; Lacey carbon with a thin, continuous carbon film</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <instrument>LEICA EM GP</instrument>
                        <details></details>
                    </vitrification>
                    <details>Empty capsid isolated from a cell lysate and purified using sucrose density gradient centrifugation.</details>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>TFS 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>
                    <c2_aperture_diameter units="µm">100.0</c2_aperture_diameter>
                    <nominal_cs units="mm">2.7</nominal_cs>
                    <nominal_defocus_min units="µm">1.0</nominal_defocus_min>
                    <calibrated_defocus_min units="µm">0.49</calibrated_defocus_min>
                    <nominal_defocus_max units="µm">3.0</nominal_defocus_max>
                    <calibrated_defocus_max units="µm">2.7</calibrated_defocus_max>
                    <nominal_magnification>81000.0</nominal_magnification>
                    <calibrated_magnification>28400.0</calibrated_magnification>
                    <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
                    <cooling_holder_cryogen>NITROGEN</cooling_holder_cryogen>
                    <alignment_procedure>
                        <coma_free/>
                    </alignment_procedure>
                    <specialist_optics>
                        <energy_filter>
                            <name>GIF Quantum LS</name>
                            <slit_width units="eV">20</slit_width>
                        </energy_filter>
                    </specialist_optics>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>GATAN K2 SUMMIT (4k x 4k)</film_or_detector_model>
                            <detector_mode>SUPER-RESOLUTION</detector_mode>
                            <digitization_details>
                                <frames_per_image>1-60</frames_per_image>
                            </digitization_details>
                            <number_grids_imaged>1</number_grids_imaged>
                            <number_real_images>1178</number_real_images>
                            <average_exposure_time units="s">15.0</average_exposure_time>
                            <average_electron_dose_per_image units="e/Å^2">138.0</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>
                <particle_selection>
                    <number_selected>8633</number_selected>
                </particle_selection>
                <ctf_correction>
                    <software_list>
                        <software>
                            <name>Bsoft</name>
                            <version>2.0.5</version>
                        </software>
                    </software_list>
                </ctf_correction>
                <startup_model type_of_model="OTHER">
                    <details>Derived from icosahedral symmetry using the maximum power algorithm in bmaxpow.</details>
                </startup_model>
                <final_reconstruction>
                    <number_classes_used>1</number_classes_used>
                    <applied_symmetry>
                        <point_group>I</point_group>
                    </applied_symmetry>
                    <algorithm>FOURIER SPACE</algorithm>
                    <resolution units="Å" res_type="BY AUTHOR">19.0</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>Bsoft</name>
                            <version>2.0.5</version>
                        </software>
                    </software_list>
                    <number_images_used>1000</number_images_used>
                </final_reconstruction>
                <initial_angle_assignment>
                    <type>OTHER</type>
                    <software_list>
                        <software>
                            <name>Bsoft</name>
                            <version>2.0.5</version>
                        </software>
                    </software_list>
                    <details>Based on icosahedral symmetry using the maximum power algorithm in bmaxpow, followed by borient.</details>
                </initial_angle_assignment>
                <final_angle_assignment>
                    <type>PROJECTION MATCHING</type>
                    <projection_matching_processing>
                        <merit_function>FRC</merit_function>
                        <angular_sampling units="degrees">0.1</angular_sampling>
                    </projection_matching_processing>
                    <software_list>
                        <software>
                            <name>Bsoft</name>
                            <version>2.0.5</version>
                        </software>
                    </software_list>
                    <details>Refinement of angular assignments with a contracting grid search to an arbitrary accuracy.</details>
                </final_angle_assignment>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="500001">
        <file>emd_22331.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>500</col>
            <row>500</row>
            <sec>500</sec>
        </dimensions>
        <origin>
            <col>-250</col>
            <row>-250</row>
            <sec>-250</sec>
        </origin>
        <spacing>
            <x>500</x>
            <y>500</y>
            <z>500</z>
        </spacing>
        <cell>
            <a units="Å">1756.0</a>
            <b units="Å">1756.0</b>
            <c units="Å">1756.0</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>-7.9673204</minimum>
            <maximum>12.287279</maximum>
            <average>0.0000000000</average>
            <std>1</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">3.512</x>
            <y units="Å">3.512</y>
            <z units="Å">3.512</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>3</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-22331::::</label>
        <annotation_details>SPN3US phage empty capsid</annotation_details>
    </map>
    <interpretation>
        <segmentation_list>
            <segmentation>
                <file>emd_22331_msk_1.map</file>
            </segmentation>
        </segmentation_list>
        <half_map_list>
            <half_map format="CCP4" size_kbytes="500001">
                <file>emd_22331_half_map_2.map.gz</file>
                <symmetry>
                    <space_group>1</space_group>
                </symmetry>
                <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
                <dimensions>
                    <col>500</col>
                    <row>500</row>
                    <sec>500</sec>
                </dimensions>
                <origin>
                    <col>-250</col>
                    <row>-250</row>
                    <sec>-250</sec>
                </origin>
                <spacing>
                    <x>500</x>
                    <y>500</y>
                    <z>500</z>
                </spacing>
                <cell>
                    <a units="Å">1756.0</a>
                    <b units="Å">1756.0</b>
                    <c units="Å">1756.0</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>-10.071663</minimum>
                    <maximum>7.5609565</maximum>
                    <average>-0.00000000000</average>
                    <std>1</std>
                </statistics>
                <pixel_spacing>
                    <x units="Å">3.512</x>
                    <y units="Å">3.512</y>
                    <z units="Å">3.512</z>
                </pixel_spacing>
                <contour_list>
                    <contour primary="true">
                        <source>AUTHOR</source>
                    </contour>
                </contour_list>
                <label>::::EMDATABANK.org::::EMD-22331::::</label>
                <annotation_details>half-volume 2</annotation_details>
            </half_map>
            <half_map format="CCP4" size_kbytes="500001">
                <file>emd_22331_half_map_1.map.gz</file>
                <symmetry>
                    <space_group>1</space_group>
                </symmetry>
                <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
                <dimensions>
                    <col>500</col>
                    <row>500</row>
                    <sec>500</sec>
                </dimensions>
                <origin>
                    <col>-250</col>
                    <row>-250</row>
                    <sec>-250</sec>
                </origin>
                <spacing>
                    <x>500</x>
                    <y>500</y>
                    <z>500</z>
                </spacing>
                <cell>
                    <a units="Å">1756.0</a>
                    <b units="Å">1756.0</b>
                    <c units="Å">1756.0</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>-10.920163</minimum>
                    <maximum>7.588113</maximum>
                    <average>0.00000000000</average>
                    <std>1</std>
                </statistics>
                <pixel_spacing>
                    <x units="Å">3.512</x>
                    <y units="Å">3.512</y>
                    <z units="Å">3.512</z>
                </pixel_spacing>
                <contour_list>
                    <contour primary="true">
                        <source>AUTHOR</source>
                    </contour>
                </contour_list>
                <label>::::EMDATABANK.org::::EMD-22331::::</label>
                <annotation_details>half-volume 1</annotation_details>
            </half_map>
        </half_map_list>
    </interpretation>
</emd>
