<emd emdb_id="EMD-5133" 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>2009-10-11</deposition>
            <header_release>2009-10-15</header_release>
            <map_release>2010-08-12</map_release>
            <update>2011-01-10</update>
        </key_dates>
        <title>17 angstrom of wild Rabbit Hemorrhagic DiseaseVirus core-like particle cryomicroscopy structure</title>
        <authors_list>
            <author>Hu Z</author>
            <author>Tian X</author>
            <author>Zhai Y</author>
            <author>Xu W</author>
            <author>Zheng D</author>
            <author>Sun F</author>
        </authors_list>
        <keywords>RHDV,vp60,vp10,core-like particles</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Hu Z</author>
                    <author order="2">Tian X</author>
                    <author order="3">Zhai Y</author>
                    <author order="4">Xu W</author>
                    <author order="5">Zheng D</author>
                    <author order="6">Sun F</author>
                    <title>Cryo-electron microscopy reconstructions of two types of wild rabbit hemorrhagic disease viruses characterized the structural features of Lagovirus.</title>
                    <journal>PROTEIN CELL</journal>
                    <volume>1</volume>
                    <first_page>48</first_page>
                    <last_page>58</last_page>
                    <year>2010</year>
                    <external_references type="PUBMED">21203997</external_references>
                    <external_references type="DOI">doi:10.1007/s13238-010-0007-0</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>wild Rabbit Hemorrhagic Disease Viruses core-like particles</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>wild Rabbit Hemorrhagic Disease Viruses core-like particles</name>
                <oligomeric_state>icosahedral</oligomeric_state>
                <number_unique_components>3</number_unique_components>
                <molecular_weight>
                    <theoretical units="MDa">7.2</theoretical>
                </molecular_weight>
            </sample_supramolecule>
            <virus_supramolecule supramolecule_id="1">
                <name synonym="rabbit hemorrhagic disease virus core like particles">rabbit hemorrhagic disease virus core like particles</name>
                <sci_species_name>rabbit hemorrhagic disease virus core like particles</sci_species_name>
                <natural_host database="NCBI">
                    <organism ncbi="9986">Oryctolagus cuniculus</organism>
                    <synonym_organism>VERTEBRATES</synonym_organism>
                </natural_host>
                <host_system database="NCBI" />
                <molecular_weight>
                    <theoretical units="MDa">7.2</theoretical>
                </molecular_weight>
                <virus_shell shell_id="1">
                    <name>S</name>
                    <diameter units="&#8491;">320</diameter>
                    <triangulation>3</triangulation>
                </virus_shell>
                <virus_type>VIROID</virus_type>
                <virus_isolate>SPECIES</virus_isolate>
                <virus_enveloped>false</virus_enveloped>
                <virus_empty>false</virus_empty>
                <syn_species_name>rabbit hemorrhagic disease virus core like particles</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">
                    <grid>
                        <details>300 mesh holygrid</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <instrument>OTHER</instrument>
                        <method>Embeded in thin layer of vitreous ice on freshly carbon-coated home-made holey EM grid by manually blotting the grids with filter paper and then plunging into liquid ethane cooled by liquid nitrogen</method>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>FEI TECNAI 20</microscope>
                    <illumination_mode>FLOOD BEAM</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>LAB6</electron_source>
                    <acceleration_voltage units="kV">200</acceleration_voltage>
                    <nominal_cs units="mm">2</nominal_cs>
                    <nominal_defocus_min units="&#181;m">2.0</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">4.0</nominal_defocus_max>
                    <nominal_magnification>50000.0</nominal_magnification>
                    <specimen_holder_model>GATAN HELIUM</specimen_holder_model>
                    <temperature>
                        <temperature_average units="K">105</temperature_average>
                    </temperature>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">KODAK SO-163 FILM</film_or_detector_model>
                            <digitization_details>
                                <sampling_interval units="&#181;m">12.7</sampling_interval>
                            </digitization_details>
                            <number_real_images>230</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">20</average_electron_dose_per_image>
                            <bits_per_pixel>16.</bits_per_pixel>
                        </image_recording>
                    </image_recording_list>
                    <specimen_holder>Eucentric</specimen_holder>
                </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;">17.0</resolution>
                    <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>Eman spider</name>
                        </software>
                    </software_list>
                    <number_images_used>895</number_images_used>
                </final_reconstruction>
                <final_two_d_classification>
                    <number_classes>21</number_classes>
                </final_two_d_classification>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="16001">
        <file>emd_5133.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>160</col>
            <row>160</row>
            <sec>160</sec>
        </dimensions>
        <origin>
            <col>-80</col>
            <row>-80</row>
            <sec>-80</sec>
        </origin>
        <spacing>
            <x>160</x>
            <y>160</y>
            <z>160</z>
        </spacing>
        <cell>
            <a units="&#8491;">406.4</a>
            <b units="&#8491;">406.4</b>
            <c units="&#8491;">406.4</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>-1.95755</minimum>
            <maximum>3.63758</maximum>
            <average>0.0550003</average>
            <std>0.848303</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">2.54</x>
            <y units="&#8491;">2.54</y>
            <z units="&#8491;">2.54</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>1.7</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>This is the cryo-electron microscopy reconstruction of the wild rabbit hemorrhagic disease virus core-like particles.</annotation_details>
        <details>::::EMDATABANK.org::::EMD-5133::::</details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <initial_model>
                    <access_code>2GH8</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>
                <target_criteria>correlation coefficient</target_criteria>
                <refinement_space>REAL</refinement_space>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>