<emd emdb_id="EMD-5454" 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>2012-08-01</deposition>
            <header_release>2013-07-03</header_release>
            <map_release>2013-10-16</map_release>
            <update>2013-10-16</update>
        </key_dates>
        <title>7 Angstrom resolution cryo-EM map of Ad5F35</title>
        <authors_list>
            <author>Cao C</author>
            <author>Dong X</author>
            <author>Wu X</author>
            <author>Ji G</author>
            <author>Cheng L</author>
            <author>Liu H</author>
        </authors_list>
        <keywords>human adenovirus, fiber, cryo-EM, near-atomic resolution</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Cao C</author>
                    <author order="2">Dong X</author>
                    <author order="3">Wu X</author>
                    <author order="4">Wen B</author>
                    <author order="5">Ji G</author>
                    <author order="6">Cheng L</author>
                    <author order="7">Liu H</author>
                    <title>Conserved fiber-penton base interaction revealed by nearly atomic resolution cryo-electron microscopy of the structure of adenovirus provides insight into receptor interaction.</title>
                    <journal>J.VIROL.</journal>
                    <volume>86</volume>
                    <first_page>12322</first_page>
                    <last_page>12329</last_page>
                    <year>2012</year>
                    <external_references type="PUBMED">22951835</external_references>
                    <external_references type="DOI">doi:10.1128/JVI.01608-12</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>Ad5F35--human adenovirus type 5 (Ad5) capsid pseudo-typed with an Ad35 fiber</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Ad5F35--human adenovirus type 5 (Ad5) capsid pseudo-typed with an Ad35 fiber</name>
                <number_unique_components>7</number_unique_components>
            </sample_supramolecule>
            <virus_supramolecule supramolecule_id="1">
                <name>Human adenovirus 5</name>
                <sci_species_name ncbi="28285">Human adenovirus 5</sci_species_name>
                <natural_host database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                    <synonym_organism>VERTEBRATES</synonym_organism>
                </natural_host>
                <host_system database="NCBI" />
                <virus_shell shell_id="1">
                    <diameter units="&#8491;">930</diameter>
                </virus_shell>
                <virus_type>VIRION</virus_type>
                <virus_isolate>STRAIN</virus_isolate>
                <virus_enveloped>false</virus_enveloped>
                <virus_empty>false</virus_empty>
            </virus_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">
                    <vitrification>
                        <cryogen_name>NITROGEN</cryogen_name>
                        <instrument>FEI VITROBOT MARK IV</instrument>
                    </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_defocus_min units="&#181;m">1.5</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">3.0</nominal_defocus_max>
                    <nominal_magnification>75000.0</nominal_magnification>
                    <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
                    <date>2010-10-09</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">GATAN ULTRASCAN 4000 (4k x 4k)</film_or_detector_model>
                            <number_real_images>4500</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">20</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <details>Viruses in the grid with thin ice were imaged with an FEI 300-kV Titan Krios cryoelectron microscope equipped with a Gatan UltraScan4000 (model 895) 16-megapixel CCD.</details>
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">7.0</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>IMIRS, recISAFs</name>
                        </software>
                    </software_list>
                    <number_images_used>2100</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
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        <file>emd_5454.map.gz</file>
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            <space_group>1</space_group>
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            <col>512</col>
            <row>512</row>
            <sec>257</sec>
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            <col>-256</col>
            <row>-256</row>
            <sec>-1</sec>
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            <a units="&#8491;">1177.6</a>
            <b units="&#8491;">1177.6</b>
            <c units="&#8491;">591.1</c>
            <alpha units="deg">90.0</alpha>
            <beta units="deg">90.0</beta>
            <gamma units="deg">90.0</gamma>
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            <fast>X</fast>
            <medium>Y</medium>
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            <minimum>-11.15326786</minimum>
            <maximum>31.068950650000001</maximum>
            <average>0.67462045</average>
            <std>3.62178588</std>
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            <x units="&#8491;">2.3</x>
            <y units="&#8491;">2.3</y>
            <z units="&#8491;">2.3</z>
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            <contour primary="true">
                <level>10.0</level>
                <source>EMDB</source>
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        <annotation_details>7 Angstrom Cryo-EM reconstruction of Ad5F35</annotation_details>
        <details>::::EMDATABANK.org::::EMD-5454::::</details>
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        <modelling_list>
            <modelling>
                <initial_model>
                    <access_code>3IYN</access_code>
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                <software_list>
                    <software>
                        <name>Chimera</name>
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                <refinement_space>REAL</refinement_space>
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        </modelling_list>
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