<emd emdb_id="EMD-5932" 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>2014-03-20</deposition>
            <header_release>2014-07-23</header_release>
            <map_release>2014-07-23</map_release>
            <update>2014-08-27</update>
        </key_dates>
        <title>Electron cryo-microscopy of Human Papillomavirus Type 16 Capsid</title>
        <authors_list>
            <author>Cardone G</author>
            <author>Moyer AL</author>
            <author>Cheng N</author>
            <author>Thompson CD</author>
            <author>Dvoretzky I</author>
            <author>Lowy DR</author>
            <author>Schiller JT</author>
            <author>Steven AC</author>
            <author>Buck CB</author>
            <author>Trus BL</author>
        </authors_list>
        <keywords />
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Cardone G</author>
                    <author order="2">Moyer AL</author>
                    <author order="3">Cheng N</author>
                    <author order="4">Thompson CD</author>
                    <author order="5">Dvoretzky I</author>
                    <author order="6">Lowy DR</author>
                    <author order="7">Schiller JT</author>
                    <author order="8">Steven AC</author>
                    <author order="9">Buck CB</author>
                    <author order="10">Trus BL</author>
                    <title>Maturation of the human papillomavirus 16 capsid.</title>
                    <journal>MBio</journal>
                    <volume>5</volume>
                    <first_page>e01104</first_page>
                    <last_page>e01114</last_page>
                    <year>2014</year>
                    <external_references type="PUBMED">25096873</external_references>
                    <external_references type="DOI">doi:10.1128/mBio.01104-14</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>3j6r</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>Human Papilloma Virus type 16 capsid</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Human Papilloma Virus type 16 capsid</name>
                <number_unique_components>1</number_unique_components>
            </sample_supramolecule>
            <virus_supramolecule supramolecule_id="1">
                <name>Human papillomavirus type 16</name>
                <sci_species_name ncbi="333760">Human papillomavirus type 16</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;">600</diameter>
                    <triangulation>7</triangulation>
                </virus_shell>
                <virus_type>VIRION</virus_type>
                <virus_isolate>SEROTYPE</virus_isolate>
                <virus_enveloped>false</virus_enveloped>
                <virus_empty>false</virus_empty>
                <sci_species_serotype>16</sci_species_serotype>
            </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>ETHANE</cryogen_name>
                        <instrument>LEICA KF80</instrument>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>FEI/PHILIPS CM200FEG</microscope>
                    <illumination_mode>FLOOD BEAM</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>FIELD EMISSION GUN</electron_source>
                    <acceleration_voltage units="kV">120</acceleration_voltage>
                    <nominal_cs units="mm">2</nominal_cs>
                    <nominal_defocus_min units="&#181;m">0.537</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">2.175</nominal_defocus_max>
                    <nominal_magnification>38000.0</nominal_magnification>
                    <specimen_holder_model>GATAN LIQUID NITROGEN</specimen_holder_model>
                    <date>2010-02-02</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="FILM">KODAK SO-163 FILM</film_or_detector_model>
                            <digitization_details>
                                <scanner>ZEISS SCAI</scanner>
                                <sampling_interval units="&#181;m">7</sampling_interval>
                            </digitization_details>
                            <number_real_images>20</number_real_images>
                            <bits_per_pixel>8.</bits_per_pixel>
                        </image_recording>
                    </image_recording_list>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <ctf_correction>
                    <details>each micrograph</details>
                </ctf_correction>
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">9.1</resolution>
                    <resolution_method>OTHER</resolution_method>
                    <software_list>
                        <software>
                            <name>Auto3DEM</name>
                        </software>
                    </software_list>
                    <number_images_used>5952</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="260612">
        <file>emd_5932.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS SIGNED INTEGER (2 BYTES)</data_type>
        <dimensions>
            <col>511</col>
            <row>511</row>
            <sec>511</sec>
        </dimensions>
        <origin>
            <col>-255</col>
            <row>-255</row>
            <sec>-255</sec>
        </origin>
        <spacing>
            <x>511</x>
            <y>511</y>
            <z>511</z>
        </spacing>
        <cell>
            <a units="&#8491;">720.51</a>
            <b units="&#8491;">720.51</b>
            <c units="&#8491;">720.51</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>-2226.0</minimum>
            <maximum>3846.0</maximum>
            <average>22.884346010000002</average>
            <std>535.922607419999963</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">1.41</x>
            <y units="&#8491;">1.41</y>
            <z units="&#8491;">1.41</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>800.0</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Reconstruction of fully mature HPV16 L1/L2 capsid</annotation_details>
        <details>::::EMDATABANK.org::::EMD-5932::::</details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <initial_model>
                    <access_code>1DZL</access_code>
                    <chain>
                        <chain_id>A</chain_id>
                    </chain>
                </initial_model>
                <refinement_protocol>FLEXIBLE FIT</refinement_protocol>
                <software_list>
                    <software>
                        <name>Chimera, PyMol, VMD, NAMD, MDFF, Bsoft</name>
                    </software>
                </software_list>
                <details>Rigid fitting of domain copies into asymmetric unit, followed by molecular dynamics-based flexible fitting, adding symmetry as constraint</details>
                <refinement_space>REAL</refinement_space>
            </modelling>
        </modelling_list>
        <figure_list>
            <figure>
                <file>emd_5932.png</file>
            </figure>
        </figure_list>
    </interpretation>
</emd>