<?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_2_2/emdb.xsd" emdb_id="EMD-8404" version="3.0.2.2">
    <admin>
        <current_status>
            <date>2021-02-03</date>
            <code>REL</code>
            <processing_site>RCSB</processing_site>
        </current_status>
        <sites>
            <deposition>RCSB</deposition>
            <last_processing>RCSB</last_processing>
        </sites>
        <key_dates>
            <deposition>2016-10-06</deposition>
            <header_release>2016-10-19</header_release>
            <map_release>2016-12-21</map_release>
            <update>2021-02-03</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)</funding_body>
                <code>P50GM082251</code>
                <country>United States</country>
            </grant_reference>
            <grant_reference>
                <funding_body>National Science Foundation (NSF, United States)</funding_body>
                <code>DMR-1310687</code>
                <country>United States</country>
            </grant_reference>
            <grant_reference>
                <funding_body>offer of the Director Grant</funding_body>
                <code>S10OD019995</code>
                <country>United States</country>
            </grant_reference>
        </grant_support>
        <title>Single particle helical reconstruction of protease cleavage product from HIV-1 Gag VLPs</title>
        <authors_list>
            <author>Fu X</author>
            <author>Zhang P</author>
        </authors_list>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Ning J</author>
                    <author order="2">Erdemci-Tandogan G</author>
                    <author order="3">Yufenyuy EL</author>
                    <author order="4">Wagner J</author>
                    <author order="5">Himes BA</author>
                    <author order="6">Zhao G</author>
                    <author order="7">Aiken C</author>
                    <author order="8">Zandi R</author>
                    <author order="9">Zhang P</author>
                    <title>In vitro protease cleavage and computer simulations reveal the HIV-1 capsid maturation pathway.</title>
                    <journal_abbreviation>Nat Commun</journal_abbreviation>
                    <country>UK</country>
                    <volume>7</volume>
                    <first_page>13689</first_page>
                    <last_page>13689</last_page>
                    <year>2016</year>
                    <external_references type="PUBMED">27958264</external_references>
                    <external_references type="DOI">doi:10.1038/ncomms13689</external_references>
                    <external_references type="ISSN">2041-1723</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-8403</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-8404</emdb_id>
                <relationship>
                    <other>associated EM volume</other>
                </relationship>
            </emdb_reference>
        </emdb_list>
    </crossreferences>
    <sample>
        <name>Single particle helical reconstruction of protease cleavage product from HIV-1 Gag VLPs</name>
        <supramolecule_list>
            <complex_supramolecule supramolecule_id="1">
                <name>Single particle helical reconstruction of protease cleavage product from HIV-1 Gag VLPs</name>
                <parent>0</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>1</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
            </complex_supramolecule>
        </supramolecule_list>
    </sample>
    <structure_determination_list>
        <structure_determination structure_determination_id="1">
            <method>helical</method>
            <aggregation_state>helicalArray</aggregation_state>
            <specimen_preparation_list>
                <helical_preparation preparation_id="1">
                    <concentration units="mg/mL">2.0</concentration>
                    <buffer>
                        <ph>6.0</ph>
                        <component>
                            <concentration units="mM">50.0</concentration>
                            <formula>NaAc</formula>
                            <name>Sodium Acetate</name>
                        </component>
                    </buffer>
                    <grid>
                        <model>Quantifoil R2/1</model>
                        <material>COPPER</material>
                        <mesh>400</mesh>
                        <support_film film_type_id="1">
                            <film_material>CARBON</film_material>
                            <film_topology>HOLEY</film_topology>
                        </support_film>
                        <pretreatment>
                            <type>GLOW DISCHARGE</type>
                        </pretreatment>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">100</chamber_humidity>
                        <chamber_temperature units="K">298</chamber_temperature>
                        <instrument>HOMEMADE PLUNGER</instrument>
                    </vitrification>
                    <details>sample is resulted from HIV-1 protease cleavage of in vitro assembled Gag VLPs</details>
                </helical_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <helical_microscopy microscopy_id="1">
                    <microscope>FEI TECNAI F20</microscope>
                    <illumination_mode>OTHER</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>FIELD EMISSION GUN</electron_source>
                    <acceleration_voltage units="kV">200</acceleration_voltage>
                    <c2_aperture_diameter units="µm">100.0</c2_aperture_diameter>
                    <nominal_cs units="mm">2.0</nominal_cs>
                    <calibrated_defocus_min units="µm">8.0</calibrated_defocus_min>
                    <calibrated_defocus_max units="µm">9.0</calibrated_defocus_max>
                    <nominal_magnification>50000.0</nominal_magnification>
                    <calibrated_magnification>66262.0</calibrated_magnification>
                    <specimen_holder_model>GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER</specimen_holder_model>
                    <cooling_holder_cryogen>NITROGEN</cooling_holder_cryogen>
                    <alignment_procedure>
                        <other/>
                    </alignment_procedure>
                    <specialist_optics>
                        <sph_aberration_corrector>No</sph_aberration_corrector>
                        <chr_aberration_corrector>No</chr_aberration_corrector>
                        <energy_filter>
                            <name>No</name>
                        </energy_filter>
                    </specialist_optics>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>GATAN ULTRASCAN 4000 (4k x 4k)</film_or_detector_model>
                            <digitization_details>
                                <dimensions>
                                    <width units="pixel">4096</width>
                                    <height units="pixel">4096</height>
                                </dimensions>
                                <sampling_interval units="µm">15.0</sampling_interval>
                            </digitization_details>
                            <number_grids_imaged>1</number_grids_imaged>
                            <number_real_images>2</number_real_images>
                            <average_exposure_time units="s">1.0</average_exposure_time>
                            <average_electron_dose_per_image units="e/Å^2">10.0</average_electron_dose_per_image>
                            <details>Image was collected by single exposure, not movie mode.</details>
                        </image_recording>
                    </image_recording_list>
                </helical_microscopy>
            </microscopy_list>
            <helical_processing image_processing_id="1">
                <image_recording_id>1</image_recording_id>
                <final_reconstruction>
                    <number_classes_used>1</number_classes_used>
                    <applied_symmetry>
                        <helical_parameters>
                            <delta_z units="Å">6.33573</delta_z>
                            <delta_phi units="deg">-129.20547</delta_phi>
                            <axial_symmetry>C1</axial_symmetry>
                        </helical_parameters>
                    </applied_symmetry>
                    <algorithm>BACK PROJECTION</algorithm>
                    <resolution units="Å" res_type="BY AUTHOR">22.0</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>IHRSH</name>
                            <version>1.5</version>
                        </software>
                    </software_list>
                    <number_images_used>863</number_images_used>
                </final_reconstruction>
                <ctf_correction>
                    <software_list>
                        <software>
                            <name>CTFFIND3</name>
                        </software>
                    </software_list>
                </ctf_correction>
                <segment_selection>
                    <number_selected>863</number_selected>
                    <software_list>
                        <software>
                            <name>EMAN</name>
                            <version>2.0</version>
                        </software>
                    </software_list>
                </segment_selection>
                <final_angle_assignment>
                    <type>NOT APPLICABLE</type>
                    <software_list>
                        <software>
                            <name>IHRSH</name>
                            <version>1.5</version>
                        </software>
                    </software_list>
                </final_angle_assignment>
            </helical_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="8789">
        <file>emd_8404.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>130</col>
            <row>130</row>
            <sec>130</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>130</x>
            <y>130</y>
            <z>130</z>
        </spacing>
        <cell>
            <a units="Å">587.6</a>
            <b units="Å">587.6</b>
            <c units="Å">587.6</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>0.47561646</minimum>
            <maximum>38.192886</maximum>
            <average>16.79996</average>
            <std>4.2317686</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">4.52</x>
            <y units="Å">4.52</y>
            <z units="Å">4.52</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>23.6</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-8404::::</label>
        <annotation_details>CA tube assembled from gag cleavage</annotation_details>
    </map>
</emd>
