<?xml version="1.0" encoding="UTF-8"?>
<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="https://ftp.ebi.ac.uk/pub/databases/em_ebi/emdb_related/emdb-schemas/emdb_schemas/v3/v3_0_8_0/emdb.xsd" version="3.0.8.0" emdb_id="EMD-0335">
    <admin>
        <current_status>
            <date>2023-10-11</date>
            <code>REL</code>
            <processing_site>RCSB</processing_site>
        </current_status>
        <sites>
            <deposition>RCSB</deposition>
            <last_processing>RCSB</last_processing>
        </sites>
        <key_dates>
            <deposition>2018-11-15</deposition>
            <header_release>2018-12-12</header_release>
            <map_release>2018-12-12</map_release>
            <update>2023-10-11</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)</funding_body>
                <code>5 P50 GM082545-10</code>
                <country>United States</country>
            </grant_reference>
            <grant_reference>
                <funding_body>National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)</funding_body>
                <code>R01 GM066087</code>
                <country>United States</country>
            </grant_reference>
            <grant_reference>
                <funding_body>National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)</funding_body>
                <code>P50 GM082545</code>
                <country>United States</country>
            </grant_reference>
            <grant_reference>
                <funding_body>National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)</funding_body>
                <code>R01 GM12850</code>
                <country>United States</country>
            </grant_reference>
        </grant_support>
        <title>MicroED Structure of the CTD-SP1 fragment of HIV-1 Gag</title>
        <authors_list>
            <author>Purdy MD</author>
            <author>Shi D</author>
        </authors_list>
        <keywords>Bevirimat, HIV-1 Gag, MicroED, Immature Hexagonal Lattice, VIRAL PROTEIN</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Purdy MD</author>
                    <author order="2">Shi D</author>
                    <author order="3">Chrustowicz J</author>
                    <author order="4">Hattne J</author>
                    <author order="5">Gonen T</author>
                    <author order="6">Yeager M</author>
                    <title>MicroED structures of HIV-1 Gag CTD-SP1 reveal binding interactions with the maturation inhibitor bevirimat.</title>
                    <journal_abbreviation>Proc. Natl. Acad. Sci. U.S.A.</journal_abbreviation>
                    <country>US</country>
                    <volume>115</volume>
                    <first_page>13258</first_page>
                    <last_page>13263</last_page>
                    <year>2018</year>
                    <external_references type="PUBMED">30530702</external_references>
                    <external_references type="DOI">doi:10.1073/pnas.1806806115</external_references>
                    <external_references type="ISSN">1091-6490</external_references>
                    <external_references type="CSD">0040</external_references>
                    <external_references type="ASTM">PNASA6</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>6n3j</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>CTD-SP1 fragment of HIV-1 Gag</name>
        <supramolecule_list>
            <complex_supramolecule supramolecule_id="1">
                <name>CTD-SP1 fragment of HIV-1 Gag</name>
                <parent>0</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>1</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <natural_source database="NCBI">
                    <organism ncbi="11676">Human immunodeficiency virus 1</organism>
                    <strain>NL4-3</strain>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">.01217387</theoretical>
                </molecular_weight>
            </complex_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>CTD-SP1 fragment of HIV-1 Gag</name>
                <natural_source database="NCBI">
                    <organism ncbi="11676">Human immunodeficiency virus 1</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.012192895</theoretical>
                </molecular_weight>
                <number_of_copies>6</number_of_copies>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="469008">Escherichia coli</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>HMHHHHHHGGSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPGATLEEMM
TACQGVGGPGHKARVLAEAMSQVTNTATIM</string>
                    <external_references type="UNIPROTKB">A0A248SMC7</external_references>
                </sequence>
            </protein_or_peptide>
        </macromolecule_list>
    </sample>
    <structure_determination_list>
        <structure_determination structure_determination_id="1">
            <method>electronCrystallography</method>
            <aggregation_state>threeDArray</aggregation_state>
            <specimen_preparation_list>
                <crystallography_preparation preparation_id="1">
                    <concentration units="mg/mL">0.8</concentration>
                    <buffer>
                        <ph>7.0</ph>
                        <component>
                            <concentration units="M">0.1</concentration>
                            <name>Bis-Tris Propane</name>
                        </component>
                        <component>
                            <concentration units="M">1.1</concentration>
                            <formula>LiSO4</formula>
                            <name>Lithium sulfate</name>
                        </component>
                    </buffer>
                    <grid>
                        <model>Quantifoil R2/4</model>
                        <material>COPPER</material>
                        <mesh>300</mesh>
                        <support_film film_type_id="1">
                            <film_material>CARBON</film_material>
                            <film_topology>HOLEY ARRAY</film_topology>
                        </support_film>
                        <pretreatment>
                            <type>GLOW DISCHARGE</type>
                            <time units="s">30</time>
                            <atmosphere>AIR</atmosphere>
                        </pretreatment>
                        <details>Glow discharge 30s each side</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <instrument>FEI VITROBOT MARK IV</instrument>
                    </vitrification>
                </crystallography_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <crystallography_microscopy microscopy_id="1">
                    <microscope>FEI TECNAI F20</microscope>
                    <illumination_mode>FLOOD BEAM</illumination_mode>
                    <imaging_mode>DIFFRACTION</imaging_mode>
                    <electron_source>FIELD EMISSION GUN</electron_source>
                    <acceleration_voltage units="kV">200</acceleration_voltage>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>TVIPS TEMCAM-F416 (4k x 4k)</film_or_detector_model>
                            <number_grids_imaged>6</number_grids_imaged>
                            <average_exposure_time units="s">8.0</average_exposure_time>
                            <average_electron_dose_per_image units="e/Å^2">0.05</average_electron_dose_per_image>
                            <details>Data from 6 crystals was merged for structure determination.</details>
                        </image_recording>
                    </image_recording_list>
                    <camera_length units="mm">2000</camera_length>
                </crystallography_microscopy>
            </microscopy_list>
            <crystallography_processing image_processing_id="1">
                <image_recording_id>1</image_recording_id>
                <final_reconstruction>
                    <resolution units="Å" res_type="BY AUTHOR">3.0</resolution>
                    <resolution_method>DIFFRACTION PATTERN/LAYERLINES</resolution_method>
                </final_reconstruction>
                <molecular_replacement>
                    <software_list>
                        <software>
                            <name>PHENIX</name>
                            <version>dev-2747</version>
                        </software>
                    </software_list>
                </molecular_replacement>
                <merging_software_list>
                    <software>
                        <name>AIMLESS</name>
                    </software>
                </merging_software_list>
                <crystallography_statistics>
                    <number_intensities_measured>10480</number_intensities_measured>
                    <number_structure_factors>10480</number_structure_factors>
                    <fourier_space_coverage>79.799999999999997</fourier_space_coverage>
                    <r_sym>0.255</r_sym>
                    <r_merge>0.564</r_merge>
                    <overall_phase_error>0</overall_phase_error>
                    <overall_phase_residual>1.0</overall_phase_residual>
                    <phase_error_rejection_criteria>0</phase_error_rejection_criteria>
                    <high_resolution units="Å">3.0</high_resolution>
                    <shell_list>
                        <shell shell_id="1">
                            <high_resolution units="Å">3.0</high_resolution>
                            <low_resolution units="Å">19.9</low_resolution>
                            <number_structure_factors>10480</number_structure_factors>
                            <phase_residual>1.0</phase_residual>
                            <fourier_space_coverage>79.799999999999997</fourier_space_coverage>
                            <multiplicity>5.7</multiplicity>
                        </shell>
                        <shell shell_id="2">
                            <high_resolution units="Å">3.0</high_resolution>
                            <low_resolution units="Å">3.2</low_resolution>
                            <number_structure_factors>1006</number_structure_factors>
                            <phase_residual>1.0</phase_residual>
                            <fourier_space_coverage>78.700000000000003</fourier_space_coverage>
                            <multiplicity>5.7</multiplicity>
                        </shell>
                    </shell_list>
                </crystallography_statistics>
            </crystallography_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="28573">
        <file>emd_0335.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>151</col>
            <row>217</row>
            <sec>218</sec>
        </dimensions>
        <origin>
            <col>-63</col>
            <row>112</row>
            <sec>-125</sec>
        </origin>
        <spacing>
            <x>218</x>
            <y>217</y>
            <z>151</z>
        </spacing>
        <cell>
            <a units="Å">99.65216</a>
            <b units="Å">97.49376</b>
            <c units="Å">71.66913</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>-4.150162</minimum>
            <maximum>3.6646461</maximum>
            <average>0.0021039585</average>
            <std>0.6012653</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">0.45712</x>
            <y units="Å">0.44928</y>
            <z units="Å">0.47463</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>1.1</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-0335::::</label>
        <annotation_details>Electron crystallographic map from 3D crystals (MicroED) of a CTD-SP1 fragment of HIV-1 Gag.</annotation_details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <initial_model>
                    <access_code>5I4T</access_code>
                    <chain>
                        <source_name>PDB</source_name>
                        <initial_model_type>experimental model</initial_model_type>
                    </chain>
                </initial_model>
                <refinement_protocol>FLEXIBLE FIT</refinement_protocol>
                <refinement_space>RECIPROCAL</refinement_space>
                <overall_bvalue>41.100000000000001</overall_bvalue>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>
