<?xml version='1.0' encoding='utf-8'?>
<emd emdb_id="EMD-25622" version="3.0.2.8" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="https://github.com/emdb-empiar/emdb-schemas/blob/master/v3/v3_0_2_8/emdb.xsd">
    <admin>
        <current_status>
            <date>2022-11-16</date>
            <code>REL</code>
            <processing_site>RCSB</processing_site>
        </current_status>
        <sites>
            <deposition>RCSB</deposition>
            <last_processing>RCSB</last_processing>
        </sites>
        <key_dates>
            <deposition>2021-12-06</deposition>
            <header_release>2022-10-19</header_release>
            <map_release>2022-10-19</map_release>
            <update>2022-11-16</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>Bill &amp; Melinda Gates Foundation</funding_body>
                <code>OPP1084519</code>
                <country>United States</country>
            </grant_reference>
            <grant_reference>
                <funding_body>Bill &amp; Melinda Gates Foundation</funding_body>
                <code>OPP1196345</code>
                <country>United States</country>
            </grant_reference>
            <grant_reference>
                <funding_body>National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)</funding_body>
                <code>UM1 Al100663</code>
                <country>United States</country>
            </grant_reference>
            <grant_reference>
                <funding_body>National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)</funding_body>
                <code>UM1 AI144462</code>
                <country>United States</country>
            </grant_reference>
        </grant_support>
        <title>Negative Stain EM reconstruction of ApexGT3 in complex with two copies of PG9 Fab</title>
        <authors_list>
            <author ORCID="0000-0003-4531-9907">Berndsen ZT</author>
        </authors_list>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Willis JR</author>
                    <author order="2">Berndsen ZT</author>
                    <author order="3">Ma KM</author>
                    <author order="4">Steichen JM</author>
                    <author order="5">Schiffner T</author>
                    <author order="6">Landais E</author>
                    <author order="7">Liguori A</author>
                    <author order="8">Kalyuzhniy O</author>
                    <author order="9">Allen JD</author>
                    <author order="10">Baboo S</author>
                    <author order="11">Omorodion O</author>
                    <author order="12">Diedrich JK</author>
                    <author order="13">Hu X</author>
                    <author order="14">Georgeson E</author>
                    <author order="15">Phelps N</author>
                    <author order="16">Eskandarzadeh S</author>
                    <author order="17">Groschel B</author>
                    <author order="18">Kubitz M</author>
                    <author order="19">Adachi Y</author>
                    <author order="20">Mullin TM</author>
                    <author order="21">Alavi NB</author>
                    <author order="22">Falcone S</author>
                    <author order="23">Himansu S</author>
                    <author order="24">Carfi A</author>
                    <author order="25">Wilson IA</author>
                    <author order="27">Paulson JC</author>
                    <author order="28">Crispin M</author>
                    <author order="29">Ward AB</author>
                    <author order="30">Schief WR</author>
                    <title>Human immunoglobulin repertoire analysis guides design of vaccine priming immunogens targeting HIV V2-apex broadly neutralizing antibody precursors.</title>
                    <journal_abbreviation>Immunity</journal_abbreviation>
                    <country>US</country>
                    <volume>55</volume>
                    <first_page>2149</first_page>
                    <last_page>2167.e9</last_page>
                    <year>2022</year>
                    <external_references type="PUBMED">36179689</external_references>
                    <external_references type="DOI">doi:10.1016/j.immuni.2022.09.001</external_references>
                    <external_references type="ISSN">1074-7613</external_references>
                    <external_references type="CSD">2048</external_references>
                    <external_references type="ASTM">IUNIEH</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-25622</emdb_id>
                <relationship>
                    <other>associated EM volume</other>
                </relationship>
            </emdb_reference>
        </emdb_list>
    </crossreferences>
    <sample>
        <name>ApexGT3 in complex with two copies of PG9 Fab</name>
        <supramolecule_list>
            <complex_supramolecule supramolecule_id="1">
                <name>ApexGT3 in complex with two copies of PG9 Fab</name>
                <parent>0</parent>
                <natural_source database="NCBI">
                    <organism ncbi="11676">Human immunodeficiency virus 1</organism>
                </natural_source>
            </complex_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>7.4</ph>
                    </buffer>
                    <staining>
                        <type>NEGATIVE</type>
                        <material>uranyl formate</material>
                    </staining>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>FEI TECNAI SPIRIT</microscope>
                    <illumination_mode>FLOOD BEAM</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>LAB6</electron_source>
                    <acceleration_voltage units="kV">120</acceleration_voltage>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>FEI EAGLE (4k x 4k)</film_or_detector_model>
                            <average_electron_dose_per_image units="e/Å^2">25.0</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>
                <final_reconstruction>
                    <applied_symmetry>
                        <point_group>C1</point_group>
                    </applied_symmetry>
                    <resolution res_type="BY AUTHOR" units="Å">26.0</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>3</version>
                        </software>
                    </software_list>
                    <number_images_used>6615</number_images_used>
                </final_reconstruction>
                <initial_angle_assignment>
                    <type>MAXIMUM LIKELIHOOD</type>
                </initial_angle_assignment>
                <final_angle_assignment>
                    <type>MAXIMUM LIKELIHOOD</type>
                </final_angle_assignment>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="4001">
        <file>emd_25622.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>100</col>
            <row>100</row>
            <sec>100</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>100</x>
            <y>100</y>
            <z>100</z>
        </spacing>
        <cell>
            <a units="Å">410.0</a>
            <b units="Å">410.0</b>
            <c units="Å">410.0</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>-0.050333265</minimum>
            <maximum>0.16690408</maximum>
            <average>7.11654e-05</average>
            <std>0.006755476</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">4.1</x>
            <y units="Å">4.1</y>
            <z units="Å">4.1</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.02</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-25622::::</label>
    </map>
    <interpretation>
        <half_map_list>
            <half_map format="CCP4" size_kbytes="4001">
                <file>emd_25622_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>100</col>
                    <row>100</row>
                    <sec>100</sec>
                </dimensions>
                <origin>
                    <col>0</col>
                    <row>0</row>
                    <sec>0</sec>
                </origin>
                <spacing>
                    <x>100</x>
                    <y>100</y>
                    <z>100</z>
                </spacing>
                <cell>
                    <a units="Å">410.0</a>
                    <b units="Å">410.0</b>
                    <c units="Å">410.0</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>-0.06389557</minimum>
                    <maximum>0.17324112</maximum>
                    <average>7.871752e-05</average>
                    <std>0.008701058</std>
                </statistics>
                <pixel_spacing>
                    <x units="Å">4.1</x>
                    <y units="Å">4.1</y>
                    <z units="Å">4.1</z>
                </pixel_spacing>
                <contour_list>
                    <contour primary="true">
                        <source>AUTHOR</source>
                    </contour>
                </contour_list>
                <label>::::EMDATABANK.org::::EMD-25622::::</label>
            </half_map>
            <half_map format="CCP4" size_kbytes="4001">
                <file>emd_25622_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>100</col>
                    <row>100</row>
                    <sec>100</sec>
                </dimensions>
                <origin>
                    <col>0</col>
                    <row>0</row>
                    <sec>0</sec>
                </origin>
                <spacing>
                    <x>100</x>
                    <y>100</y>
                    <z>100</z>
                </spacing>
                <cell>
                    <a units="Å">410.0</a>
                    <b units="Å">410.0</b>
                    <c units="Å">410.0</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>-0.06626868</minimum>
                    <maximum>0.1838868</maximum>
                    <average>6.7008354e-05</average>
                    <std>0.008641325</std>
                </statistics>
                <pixel_spacing>
                    <x units="Å">4.1</x>
                    <y units="Å">4.1</y>
                    <z units="Å">4.1</z>
                </pixel_spacing>
                <contour_list>
                    <contour primary="true">
                        <source>AUTHOR</source>
                    </contour>
                </contour_list>
                <label>::::EMDATABANK.org::::EMD-25622::::</label>
            </half_map>
        </half_map_list>
    </interpretation>
</emd>