<emd emdb_id="EMD-5294" version="3.0.1.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="https://github.com/emdb-empiar/emdb-schemas/blob/master/v3/v3_0_1_1/emdb_relaxed.xsd">
    <admin>
        <current_status>
            <code>REL</code>
            <processing_site>RCSB</processing_site>
        </current_status>
        <sites>
            <deposition>RCSB</deposition>
            <last_processing>RCSB</last_processing>
        </sites>
        <key_dates>
            <deposition>2011-05-22</deposition>
            <header_release>2011-10-26</header_release>
            <map_release>2012-05-29</map_release>
            <update>2012-05-29</update>
        </key_dates>
        <title>3D reconstruction of frozen hydrated HIV-1 integrase dimer in complex with two Fabs.</title>
        <authors_list>
            <author>Wu S</author>
            <author>Avila-Sakar A</author>
            <author>Kim J</author>
            <author>Booth DS</author>
            <author>Greenberg CH</author>
            <author>Rossi A</author>
            <author>Liao M</author>
            <author>Alian A</author>
            <author>Griner SL</author>
            <author>Juge N</author>
            <author>Mergel CM</author>
            <author>Chaparro-Riggers J</author>
            <author>Strop P</author>
            <author>Tampe R</author>
            <author>Edwards RH</author>
            <author>Stroud RM</author>
            <author>Craik CS</author>
            <author>Cheng Y</author>
        </authors_list>
        <keywords>HIV-1 integrase dimer, Fab</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Wu S</author>
                    <author order="2">Avila-Sakar A</author>
                    <author order="3">Kim J</author>
                    <author order="4">Booth DS</author>
                    <author order="5">Greenberg CH</author>
                    <author order="6">Rossi A</author>
                    <author order="7">Liao M</author>
                    <author order="8">Li X</author>
                    <author order="9">Alian A</author>
                    <author order="10">Griner SL</author>
                    <author order="11">Juge N</author>
                    <author order="12">Yu Y</author>
                    <author order="13">Mergel CM</author>
                    <author order="14">Chaparro-Riggers J</author>
                    <author order="15">Strop P</author>
                    <author order="16">Tampe R</author>
                    <author order="17">Edwards RH</author>
                    <author order="18">Stroud RM</author>
                    <author order="19">Craik CS</author>
                    <author order="20">Cheng Y</author>
                    <title>Fabs enable single particle cryoEM studies of small proteins.</title>
                    <journal>STRUCTURE</journal>
                    <volume>20</volume>
                    <first_page>582</first_page>
                    <last_page>592</last_page>
                    <year>2012</year>
                    <external_references type="PUBMED">22483106</external_references>
                    <external_references type="DOI">doi:10.1016/j.str.2012.02.017</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>HIV-1 integrase - Fab complex</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>HIV-1 integrase - Fab complex</name>
                <oligomeric_state>2 Fabs bind to one integrase dimer</oligomeric_state>
                <number_unique_components>2</number_unique_components>
                <molecular_weight>
                    <experimental units="MDa">0.16</experimental>
                    <theoretical units="MDa">0.16</theoretical>
                </molecular_weight>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>integrase</name>
                <natural_source database="NCBI">
                    <organism ncbi="11676">Human immunodeficiency virus 1</organism>
                    <synonym_organism>HIV-1</synonym_organism>
                </natural_source>
                <molecular_weight>
                    <experimental units="MDa">0.032</experimental>
                    <theoretical units="MDa">0.032</theoretical>
                </molecular_weight>
                <details>dimer, total molecular weight 65kDa</details>
                <number_of_copies>2</number_of_copies>
                <oligomeric_state>dimer</oligomeric_state>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                </recombinant_expression>
                <sequence />
            </protein_or_peptide>
        </macromolecule_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">
                    <grid>
                        <details>200 mesh Quantifoil</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">100</chamber_humidity>
                        <chamber_temperature units="K">100</chamber_temperature>
                        <instrument>OTHER</instrument>
                        <details>Vitrification instrument: Vitrobot</details>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>FEI TECNAI F20</microscope>
                    <illumination_mode>FLOOD BEAM</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>FIELD EMISSION GUN</electron_source>
                    <acceleration_voltage units="kV">200</acceleration_voltage>
                    <nominal_cs units="mm">2.1</nominal_cs>
                    <nominal_defocus_min units="&#181;m">2.0</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">5.0</nominal_defocus_max>
                    <nominal_magnification>80000.0</nominal_magnification>
                    <specimen_holder_model>GATAN LIQUID NITROGEN</specimen_holder_model>
                    <date>2011-02-01</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">TVIPS TEMCAM-F816 (8k x 8k)</film_or_detector_model>
                            <average_electron_dose_per_image units="e/&#8491;^2">30</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                    <specimen_holder>CT3500</specimen_holder>
                    <tilt_angle_min>0</tilt_angle_min>
                    <tilt_angle_max>0</tilt_angle_max>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <ctf_correction>
                    <details>Each particle</details>
                </ctf_correction>
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">9.6</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>Frealign</name>
                        </software>
                    </software_list>
                    <number_images_used>14000</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="12665">
        <file>emd_5294.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>148</col>
            <row>148</row>
            <sec>148</sec>
        </dimensions>
        <origin>
            <col>-54</col>
            <row>-74</row>
            <sec>-74</sec>
        </origin>
        <spacing>
            <x>148</x>
            <y>148</y>
            <z>148</z>
        </spacing>
        <cell>
            <a units="&#8491;">266.4</a>
            <b units="&#8491;">266.4</b>
            <c units="&#8491;">266.4</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>-1.03870511</minimum>
            <maximum>3.12253904</maximum>
            <average>-0.00818645</average>
            <std>0.18489794</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">1.8</x>
            <y units="&#8491;">1.8</y>
            <z units="&#8491;">1.8</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>1.0</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>This is 3D reconstruction of frozen hydrated HIV-1 integrase dimer in complex with 2 Fabs.</annotation_details>
        <details>::::EMDATABANK.org::::EMD-5294::::</details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <initial_model>
                    <access_code>1EXQ</access_code>
                </initial_model>
                <refinement_protocol>RIGID BODY FIT</refinement_protocol>
                <software_list>
                    <software>
                        <name>Chimera</name>
                    </software>
                </software_list>
                <details>Protocol: rigid body</details>
                <refinement_space>REAL</refinement_space>
            </modelling>
            <modelling>
                <initial_model>
                    <access_code>1M71</access_code>
                </initial_model>
                <refinement_protocol>RIGID BODY FIT</refinement_protocol>
                <software_list>
                    <software>
                        <name>Chimera</name>
                    </software>
                </software_list>
                <details>Protocol: rigid body</details>
                <refinement_space>REAL</refinement_space>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>