<emd emdb_id="EMD-5142" 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>2009-11-21</deposition>
            <header_release>2010-04-26</header_release>
            <map_release>2010-04-26</map_release>
            <update>2010-06-21</update>
        </key_dates>
        <title>Ab initio reconstruction of the avian polyomavirus via the asymmetric random-model method</title>
        <authors_list>
            <author>Sanz E</author>
            <author>Stewart AB</author>
            <author>Belnap DM</author>
        </authors_list>
        <keywords>random-model method, ab initio reconstruction, avian polyomavirus</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Sanz Garcia E</author>
                    <author order="2">Stewart AB</author>
                    <author order="3">Belnap DM</author>
                    <title>The random-model method enables ab initio 3D reconstruction of asymmetric particles and determination of particle symmetry.</title>
                    <journal>J.STRUCT.BIOL.</journal>
                    <volume>171</volume>
                    <first_page>216</first_page>
                    <last_page>222</last_page>
                    <year>2010</year>
                    <external_references type="PUBMED">20353825</external_references>
                    <external_references type="DOI">doi:10.1016/j.jsb.2010.03.017</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>Avian polyomavirus</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Avian polyomavirus</name>
                <number_unique_components>1</number_unique_components>
            </sample_supramolecule>
            <virus_supramolecule supramolecule_id="1">
                <name synonym="Avian polyomavirus">Avian polyomavirus</name>
                <sci_species_name>Avian polyomavirus</sci_species_name>
                <natural_host database="NCBI">
                    <organism ncbi="8782">Aves</organism>
                    <synonym_organism>VERTEBRATES</synonym_organism>
                </natural_host>
                <host_system database="NCBI" />
                <virus_shell shell_id="1">
                    <name>VP1</name>
                    <diameter units="&#8491;">520</diameter>
                    <triangulation>7</triangulation>
                </virus_shell>
                <virus_type>VIRION</virus_type>
                <virus_isolate>STRAIN</virus_isolate>
                <virus_enveloped>false</virus_enveloped>
                <virus_empty>false</virus_empty>
                <syn_species_name>Avian polyomavirus</syn_species_name>
            </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>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 F30</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_defocus_min units="&#181;m">0.7</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">4.9</nominal_defocus_max>
                    <nominal_magnification>39000.0</nominal_magnification>
                    <specimen_holder_model>GATAN LIQUID NITROGEN</specimen_holder_model>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="FILM">KODAK SO-163 FILM</film_or_detector_model>
                            <digitization_details>
                                <scanner>NIKON SUPER COOLSCAN 9000</scanner>
                                <sampling_interval units="&#181;m">6.3</sampling_interval>
                            </digitization_details>
                        </image_recording>
                    </image_recording_list>
                    <specimen_holder>Eucentric</specimen_holder>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <ctf_correction>
                    <details>None</details>
                </ctf_correction>
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">35.0</resolution>
                    <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>PFT3DR, Bsoft</name>
                        </software>
                    </software_list>
                    <details>Random-model method. Angular step-size was initially set to 20 deg. in the first iteration and gradually decreased by 0.19 deg. in each successive iteration, until a lower limit of 1 deg. was reached.</details>
                    <number_images_used>4198</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="193091">
        <file>emd_5142.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>367</col>
            <row>367</row>
            <sec>367</sec>
        </dimensions>
        <origin>
            <col>-183</col>
            <row>-183</row>
            <sec>-183</sec>
        </origin>
        <spacing>
            <x>367</x>
            <y>367</y>
            <z>367</z>
        </spacing>
        <cell>
            <a units="&#8491;">598.21</a>
            <b units="&#8491;">598.21</b>
            <c units="&#8491;">598.21</c>
            <alpha units="deg">90</alpha>
            <beta units="deg">90</beta>
            <gamma units="deg">90</gamma>
        </cell>
        <axis_order>
            <fast>X</fast>
            <medium>Y</medium>
            <slow>Z</slow>
        </axis_order>
        <statistics>
            <minimum>-2.49513</minimum>
            <maximum>3.13667</maximum>
            <average>0.000389735</average>
            <std>0.489641</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">1.63</x>
            <y units="&#8491;">1.63</y>
            <z units="&#8491;">1.63</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.722</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>The avian polyomavirus</annotation_details>
        <details>::::EMDATABANK.org::::EMD-5142::::</details>
    </map>
</emd>