<emd emdb_id="EMD-6324" 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>2015-04-21</deposition>
            <header_release>2015-05-06</header_release>
            <map_release>2015-07-22</map_release>
            <update>2015-07-22</update>
        </key_dates>
        <title>Electron cryo-microscopy of T4 portal protein</title>
        <authors_list>
            <author>Sun L</author>
            <author>Zhang X</author>
            <author>Gao S</author>
            <author>Rao PA</author>
            <author>Padilla-Sanchez V</author>
            <author>Chen Z</author>
            <author>Sun S</author>
            <author>Xiang Y</author>
            <author>Sriram S</author>
            <author>Rao VB</author>
            <author>Rossmann MG</author>
        </authors_list>
        <keywords>T4 portal protein</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Sun L</author>
                    <author order="2">Zhang X</author>
                    <author order="3">Gao S</author>
                    <author order="4">Rao PA</author>
                    <author order="5">Padilla-Sanchez V</author>
                    <author order="6">Chen Z</author>
                    <author order="7">Sun S</author>
                    <author order="8">Xiang Y</author>
                    <author order="9">Subramaniam S</author>
                    <author order="10">Rao VB</author>
                    <author order="11">Rossmann MG</author>
                    <title>Cryo-EM structure of the bacteriophage T4 portal protein assembly at near-atomic resolution.</title>
                    <journal>Nat.Commun.</journal>
                    <volume>6</volume>
                    <first_page>7548</first_page>
                    <last_page>7548</last_page>
                    <year>2015</year>
                    <external_references type="PUBMED">26144253</external_references>
                    <external_references type="DOI">doi:10.1038/ncomms8548</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>3ja7</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>T4 portal protein gp20</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>T4 portal protein gp20</name>
                <oligomeric_state>dodecamer</oligomeric_state>
                <number_unique_components>1</number_unique_components>
                <molecular_weight>
                    <experimental units="MDa">0.66</experimental>
                </molecular_weight>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name synonym="connector">T4 Portal protein gp20</name>
                <natural_source database="NCBI">
                    <organism ncbi="10665">Enterobacteria phage T4</organism>
                    <synonym_organism>phage T4</synonym_organism>
                </natural_source>
                <molecular_weight>
                    <experimental units="MDa">0.66</experimental>
                </molecular_weight>
                <number_of_copies>12</number_of_copies>
                <oligomeric_state>dodecamer</oligomeric_state>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="469008">Escherichia coli BL21(DE3)</recombinant_organism>
                    <recombinant_strain>BL21(DE3) pLysS</recombinant_strain>
                    <recombinant_plasmid>pCDFDuet-1</recombinant_plasmid>
                </recombinant_expression>
                <sequence>
                    <external_references type="UNIPROTKB">P13334</external_references>
                </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">
                    <concentration units="mg/mL">1.0</concentration>
                    <buffer>
                        <ph>7.8</ph>
                        <details>20 mM Tris, 400 mM NaCl, 5 mM EDTA</details>
                    </buffer>
                    <grid>
                        <details>Quantifoil R1.2/1.3 holey carbon on 200 mesh copper</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">90</chamber_humidity>
                        <chamber_temperature units="K">120</chamber_temperature>
                        <instrument>GATAN CRYOPLUNGE 3</instrument>
                        <method>Blot for 7 seconds before plunging</method>
                    </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="&#181;m">1.5</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">2.5</nominal_defocus_max>
                    <nominal_magnification>29000.0</nominal_magnification>
                    <calibrated_magnification>50000.0</calibrated_magnification>
                    <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
                    <temperature>
                        <temperature_min units="K">80</temperature_min>
                        <temperature_max units="K">105</temperature_max>
                        <temperature_average units="K">100</temperature_average>
                    </temperature>
                    <specialist_optics>
                        <energy_filter>
                            <name>Gatan</name>
                            <lower_energy_threshold units="eV">0.0</lower_energy_threshold>
                            <upper_energy_threshold units="eV">25.0</upper_energy_threshold>
                        </energy_filter>
                    </specialist_optics>
                    <date>2014-07-10</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">GATAN K2 (4k x 4k)</film_or_detector_model>
                            <number_real_images>839</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">2</average_electron_dose_per_image>
                            <details>Every image is the average of 11 frames recorded by the direct electron detector.</details>
                            <bits_per_pixel>8.</bits_per_pixel>
                        </image_recording>
                    </image_recording_list>
                    <specimen_holder>Liquid nitrogen-cooled</specimen_holder>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <details>The particles were selected using an automatic selection program.</details>
                <ctf_correction>
                    <details>each particle</details>
                </ctf_correction>
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">3.6</resolution>
                    <resolution_method>OTHER</resolution_method>
                    <software_list>
                        <software>
                            <name>Relion</name>
                        </software>
                    </software_list>
                    <number_images_used>98000</number_images_used>
                </final_reconstruction>
                <final_two_d_classification>
                    <number_classes>15</number_classes>
                </final_two_d_classification>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="78609">
        <file>emd_6324.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>272</col>
            <row>272</row>
            <sec>272</sec>
        </dimensions>
        <origin>
            <col>-136</col>
            <row>-136</row>
            <sec>-136</sec>
        </origin>
        <spacing>
            <x>272</x>
            <y>272</y>
            <z>272</z>
        </spacing>
        <cell>
            <a units="&#8491;">272.0</a>
            <b units="&#8491;">272.0</b>
            <c units="&#8491;">272.0</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>-0.09168965</minimum>
            <maximum>0.13901675</maximum>
            <average>0.00052522</average>
            <std>0.00507363</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">1.0</x>
            <y units="&#8491;">1.0</y>
            <z units="&#8491;">1.0</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.016</level>
                <source>EMDB</source>
            </contour>
        </contour_list>
        <annotation_details>Reconstruction of T4 portal protein gp20</annotation_details>
        <details>::::EMDATABANK.org::::EMD-6324::::</details>
    </map>
</emd>