<emd emdb_id="EMD-5425" 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>2012-05-29</deposition>
            <header_release>2012-06-04</header_release>
            <map_release>2012-06-04</map_release>
            <update>2012-06-04</update>
        </key_dates>
        <title>Cryo-EM reconstruction of fully-mature capsid of Nudaurelia capensis omega virus (NwV)</title>
        <authors_list>
            <author>Matsui T</author>
            <author>Lander GC</author>
            <author>Khayat R</author>
            <author>Johnson JE</author>
        </authors_list>
        <keywords>T=4, quasi-equivalence, maturation</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Matsui T</author>
                    <author order="2">Lander GC</author>
                    <author order="3">Khayat R</author>
                    <author order="4">Johnson JE</author>
                    <title>Subunits fold at position-dependent rates during maturation of a eukaryotic RNA virus.</title>
                    <journal>PROC.NAT.ACAD.SCI.USA</journal>
                    <volume>107</volume>
                    <first_page>14111</first_page>
                    <last_page>14115</last_page>
                    <year>2010</year>
                    <external_references type="PUBMED">20660783</external_references>
                    <external_references type="DOI">doi:10.1073/pnas.1004221107</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>Fully-mature capsid of Nudaurelia capensis omega virus (NwV)</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Fully-mature capsid of Nudaurelia capensis omega virus (NwV)</name>
                <oligomeric_state>Icosahedral virus</oligomeric_state>
                <number_unique_components>1</number_unique_components>
            </sample_supramolecule>
            <virus_supramolecule supramolecule_id="1">
                <name synonym="NwV (N omega V)">Nudaurelia capensis omega virus</name>
                <sci_species_name ncbi="12541">Nudaurelia capensis omega virus</sci_species_name>
                <natural_host database="NCBI">
                    <organism ncbi="7088">Lepidoptera</organism>
                    <synonym_organism>INVERTEBRATES</synonym_organism>
                </natural_host>
                <host_system database="NCBI" />
                <virus_shell shell_id="1">
                    <diameter units="&#8491;">400</diameter>
                    <triangulation>4</triangulation>
                </virus_shell>
                <virus_type>VIRUS-LIKE PARTICLE</virus_type>
                <virus_isolate>STRAIN</virus_isolate>
                <virus_enveloped>false</virus_enveloped>
                <virus_empty>false</virus_empty>
                <syn_species_name>NwV (N omega V)</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">
                    <concentration units="mg/mL">20</concentration>
                    <buffer>
                        <ph>5.0</ph>
                        <details>50mM NaOAc, 250mM NaCl</details>
                    </buffer>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">100</chamber_humidity>
                        <chamber_temperature units="K">90</chamber_temperature>
                        <instrument>FEI VITROBOT MARK I</instrument>
                        <method>Blot for 4sec before plunging</method>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>FEI TECNAI F20</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_defocus_min units="&#181;m">1.0</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">3.0</nominal_defocus_max>
                    <nominal_magnification>80000.0</nominal_magnification>
                    <specimen_holder_model>GATAN LIQUID NITROGEN</specimen_holder_model>
                    <date>2007-06-19</date>
                    <image_recording_list>
                        <image_recording>
                            <number_real_images>228</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">16.5</average_electron_dose_per_image>
                            <details>Data were collected using the Leginon automated electron microscopy package and data processing was performed using the Appion pipeline.</details>
                        </image_recording>
                    </image_recording_list>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <ctf_correction>
                    <details>Each image</details>
                </ctf_correction>
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">9.8</resolution>
                    <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>EMAN</name>
                        </software>
                    </software_list>
                    <details>Data processing was performed using the Appion pipeline.</details>
                    <number_images_used>24514</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="31251">
        <file>emd_5425.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>200</col>
            <row>200</row>
            <sec>200</sec>
        </dimensions>
        <origin>
            <col>-100</col>
            <row>-100</row>
            <sec>-100</sec>
        </origin>
        <spacing>
            <x>200</x>
            <y>200</y>
            <z>200</z>
        </spacing>
        <cell>
            <a units="&#8491;">553.6</a>
            <b units="&#8491;">553.6</b>
            <c units="&#8491;">553.6</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>-4.06927013</minimum>
            <maximum>6.41802597</maximum>
            <average>0.0</average>
            <std>1.0</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">2.768</x>
            <y units="&#8491;">2.768</y>
            <z units="&#8491;">2.768</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>1.0</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Reconstruction of fully mature NwV capsid</annotation_details>
        <details>::::EMDATABANK.org::::EMD-5425::::</details>
    </map>
</emd>