<?xml version='1.0' encoding='utf-8'?>
<emd emdb_id="EMD-0050" 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>2019-04-03</date>
            <code>REL</code>
            <processing_site>PDBe</processing_site>
        </current_status>
        <sites>
            <deposition>PDBe</deposition>
            <last_processing>PDBe</last_processing>
        </sites>
        <key_dates>
            <deposition>2018-06-13</deposition>
            <header_release>2018-08-22</header_release>
            <map_release>2019-03-27</map_release>
            <update>2019-04-03</update>
        </key_dates>
        <title>DNA-devoid HCIV-1 virus particle</title>
        <authors_list>
            <author>Santos-Perez I</author>
            <author>Charro D</author>
            <author>Gil-Carton D</author>
            <author>Azkargorta M</author>
            <author>Elortza F</author>
            <author>Bamford DH</author>
            <author>Oksanen HM</author>
            <author>Abrescia NGA</author>
        </authors_list>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Santos-Perez I</author>
                    <author order="2">Charro D</author>
                    <author order="3">Gil-Carton D</author>
                    <author order="4">Azkargorta M</author>
                    <author order="5">Elortza F</author>
                    <author order="6">Bamford DH</author>
                    <author order="7">Oksanen HM</author>
                    <author order="8">Abrescia NGA</author>
                    <title>Structural basis for assembly of vertical single beta-barrel viruses.</title>
                    <journal_abbreviation>Nat Commun</journal_abbreviation>
                    <country>UK</country>
                    <volume>10</volume>
                    <first_page>1184</first_page>
                    <last_page>1184</last_page>
                    <year>2019</year>
                    <external_references type="PUBMED">30862777</external_references>
                    <external_references type="DOI">doi:10.1038/s41467-019-08927-2</external_references>
                    <external_references type="ISSN">2041-1723</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-0050</emdb_id>
                <relationship>
                    <other>associated EM volume</other>
                </relationship>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-0072</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-0073</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-0131</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-0174</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-0172</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
            </emdb_reference>
        </emdb_list>
    </crossreferences>
    <sample>
        <name>Haloarcula californiae ATCC 33799</name>
        <supramolecule_list>
            <virus_supramolecule supramolecule_id="1">
                <name>Haloarcula californiae ATCC 33799</name>
                <parent>0</parent>
                <details>Haloarcula californiae icosahedral virus - 1</details>
                <sci_species_name ncbi="662475">Haloarcula californiae ATCC 33799</sci_species_name>
                <natural_host database="NCBI">
                    <organism ncbi="662475">Haloarcula californiae ATCC 33799</organism>
                </natural_host>
                <virus_shell shell_id="1">
                    <diameter units="Å">800.0</diameter>
                    <triangulation>28</triangulation>
                </virus_shell>
                <virus_type>VIRION</virus_type>
                <virus_isolate>SPECIES</virus_isolate>
                <virus_enveloped>false</virus_enveloped>
                <virus_empty>true</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">1.2</concentration>
                    <buffer>
                        <ph>7.2</ph>
                        <component>
                            <concentration units="M">1.0</concentration>
                            <formula>NaCl</formula>
                            <name>Sodium Chloride</name>
                        </component>
                        <component>
                            <concentration units="mM">70.0</concentration>
                            <formula>MgCl2</formula>
                            <name>Magnesium Chloride</name>
                        </component>
                        <component>
                            <concentration units="mM">20.0</concentration>
                            <formula>KCl</formula>
                            <name>Potasium Chloride</name>
                        </component>
                        <component>
                            <concentration units="mM">1.0</concentration>
                            <formula>CaCl2</formula>
                            <name>Calcium Chloride</name>
                        </component>
                        <component>
                            <concentration units="mM">50.0</concentration>
                            <formula>C4H11NO3</formula>
                            <name>Tris-HCl</name>
                        </component>
                    </buffer>
                    <grid>
                        <model>Quantifoil R1.2/1.3</model>
                        <material>COPPER</material>
                        <mesh>200</mesh>
                        <support_film film_type_id="1">
                            <film_material>CARBON</film_material>
                            <film_topology>HOLEY</film_topology>
                        </support_film>
                        <pretreatment>
                            <type>PLASMA CLEANING</type>
                        </pretreatment>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <instrument>FEI VITROBOT MARK III</instrument>
                        <details />
                    </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">300</acceleration_voltage>
                    <nominal_cs units="mm">2.7</nominal_cs>
                    <nominal_defocus_min units="µm">0.6</nominal_defocus_min>
                    <nominal_defocus_max units="µm">3.9</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>FEI FALCON II (4k x 4k)</film_or_detector_model>
                            <detector_mode>INTEGRATING</detector_mode>
                            <digitization_details>
                                <frames_per_image>1-26</frames_per_image>
                            </digitization_details>
                            <number_grids_imaged>1</number_grids_imaged>
                            <number_real_images>3218</number_real_images>
                            <average_electron_dose_per_image units="e/Å^2">36.0</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>4584</number_selected>
                </particle_selection>
                <ctf_correction>
                    <software_list>
                        <software>
                            <name>CTFFIND</name>
                            <version>4</version>
                        </software>
                    </software_list>
                </ctf_correction>
                <startup_model type_of_model="OTHER">
                    <details>Associate ENTRY (HCIV-1).</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 res_type="BY AUTHOR" units="Å">14.9</resolution>
                    <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>2.0</version>
                        </software>
                    </software_list>
                    <number_images_used>84</number_images_used>
                </final_reconstruction>
                <initial_angle_assignment>
                    <type>PROJECTION MATCHING</type>
                    <projection_matching_processing />
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>2.0</version>
                        </software>
                    </software_list>
                </initial_angle_assignment>
                <final_angle_assignment>
                    <type>PROJECTION MATCHING</type>
                    <projection_matching_processing />
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>2.0</version>
                        </software>
                    </software_list>
                </final_angle_assignment>
                <final_three_d_classification>
                    <number_classes>10</number_classes>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>2.0</version>
                        </software>
                    </software_list>
                </final_three_d_classification>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="226493">
        <file>emd_0050.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>384</col>
            <row>384</row>
            <sec>384</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>384</x>
            <y>384</y>
            <z>384</z>
        </spacing>
        <cell>
            <a units="Å">1075.2</a>
            <b units="Å">1075.2</b>
            <c units="Å">1075.2</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>-0.31705016</minimum>
            <maximum>1.104037</maximum>
            <average>0.0006336519</average>
            <std>0.042282388</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">2.8</x>
            <y units="Å">2.8</y>
            <z units="Å">2.8</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.135</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-0050::::</label>
        <annotation_details>This map corresponds to DNA-devoid HCIV-1 particles. A cut through shows the lack of DNA and the unexpanded membrane vesicle. To better distinguish the membrane it is advisable to filter to 10 Ang.</annotation_details>
    </map>
    <interpretation>
        <half_map_list>
            <half_map format="CCP4" size_kbytes="226493">
                <file>emd_0050_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>384</col>
                    <row>384</row>
                    <sec>384</sec>
                </dimensions>
                <origin>
                    <col>0</col>
                    <row>0</row>
                    <sec>0</sec>
                </origin>
                <spacing>
                    <x>384</x>
                    <y>384</y>
                    <z>384</z>
                </spacing>
                <cell>
                    <a units="Å">1075.2</a>
                    <b units="Å">1075.2</b>
                    <c units="Å">1075.2</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>-0.072725885</minimum>
                    <maximum>0.2162126</maximum>
                    <average>0.0003447527</average>
                    <std>0.012872897</std>
                </statistics>
                <pixel_spacing>
                    <x units="Å">2.8</x>
                    <y units="Å">2.8</y>
                    <z units="Å">2.8</z>
                </pixel_spacing>
                <contour_list>
                    <contour primary="true">
                        <source>AUTHOR</source>
                    </contour>
                </contour_list>
                <label>::::EMDATABANK.org::::EMD-0050::::</label>
            </half_map>
            <half_map format="CCP4" size_kbytes="226493">
                <file>emd_0050_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>384</col>
                    <row>384</row>
                    <sec>384</sec>
                </dimensions>
                <origin>
                    <col>0</col>
                    <row>0</row>
                    <sec>0</sec>
                </origin>
                <spacing>
                    <x>384</x>
                    <y>384</y>
                    <z>384</z>
                </spacing>
                <cell>
                    <a units="Å">1075.2</a>
                    <b units="Å">1075.2</b>
                    <c units="Å">1075.2</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>-0.06813132</minimum>
                    <maximum>0.10705959</maximum>
                    <average>0.00028889923</average>
                    <std>0.011921769</std>
                </statistics>
                <pixel_spacing>
                    <x units="Å">2.8</x>
                    <y units="Å">2.8</y>
                    <z units="Å">2.8</z>
                </pixel_spacing>
                <contour_list>
                    <contour primary="true">
                        <source>AUTHOR</source>
                    </contour>
                </contour_list>
                <label>::::EMDATABANK.org::::EMD-0050::::</label>
            </half_map>
        </half_map_list>
    </interpretation>
</emd>