<emd emdb_id="EMD-2043" 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>PDBe</processing_site>
        </current_status>
        <sites>
            <deposition>PDBe</deposition>
            <last_processing>PDBe</last_processing>
        </sites>
        <key_dates>
            <deposition>2012-02-08</deposition>
            <header_release>2012-02-15</header_release>
            <map_release>2012-03-08</map_release>
            <update>2012-03-08</update>
        </key_dates>
        <title>Subtomogram averaging reconstruction of the Ebola virus nucleocapsid</title>
        <authors_list>
            <author>Bharat TAM</author>
            <author>Noda T</author>
            <author>Riches JD</author>
            <author>Kraehling V</author>
            <author>Kolesnikova L</author>
            <author>Becker S</author>
            <author>Kawaoka Y</author>
            <author>Briggs JAG</author>
        </authors_list>
        <keywords>ebola virus, nucleocapsid, subtomogram averaging</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Bharat TA</author>
                    <author order="2">Noda T</author>
                    <author order="3">Riches JD</author>
                    <author order="4">Kraehling V</author>
                    <author order="5">Kolesnikova L</author>
                    <author order="6">Becker S</author>
                    <author order="7">Kawaoka Y</author>
                    <author order="8">Briggs JA</author>
                    <title>Structural dissection of Ebola virus and its assembly determinants using cryo-electron tomography.</title>
                    <journal>PROC.NAT.ACAD.SCI.USA</journal>
                    <volume>109</volume>
                    <first_page>4275</first_page>
                    <last_page>4280</last_page>
                    <year>2012</year>
                    <external_references type="PUBMED">22371572</external_references>
                    <external_references type="DOI">doi:10.1073/pnas.1120453109</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>Ebola virus nucleocapsid</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Ebola virus nucleocapsid</name>
                <number_unique_components>1</number_unique_components>
            </sample_supramolecule>
            <virus_supramolecule supramolecule_id="1">
                <name>Zaire ebolavirus</name>
                <sci_species_name ncbi="186538">Zaire ebolavirus</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_type>VIRION</virus_type>
                <virus_isolate>SPECIES</virus_isolate>
                <virus_enveloped>true</virus_enveloped>
                <virus_empty>false</virus_empty>
            </virus_supramolecule>
        </supramolecule_list>
    </sample>
    <structure_determination_list>
        <structure_determination structure_determination_id="1">
            <method>subtomogramAveraging</method>
            <aggregation_state>filament</aggregation_state>
            <specimen_preparation_list>
                <subtomogram_averaging_preparation preparation_id="1">
                    <buffer>
                        <ph>7.0</ph>
                        <details>PBS buffer with 4% paraformaldehyde</details>
                    </buffer>
                    <grid>
                        <details>300 mesh holey carbon C-Flat grid with 2micron holes.</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <instrument>HOMEMADE PLUNGER</instrument>
                    </vitrification>
                </subtomogram_averaging_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <subtomogram_averaging_microscopy microscopy_id="1">
                    <microscope>FEI POLARA 300</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_cs units="mm">2.0</nominal_cs>
                    <nominal_defocus_min units="&#181;m">-4.0</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">-6.0</nominal_defocus_max>
                    <nominal_magnification>27500.0</nominal_magnification>
                    <specimen_holder_model>OTHER</specimen_holder_model>
                    <alignment_procedure>
                        <legacy>
                            <astigmatism>Objective lens astigmatism was corrected at high magnification.</astigmatism>
                        </legacy>
                    </alignment_procedure>
                    <specialist_optics>
                        <energy_filter>
                            <name>Gatan (GIF 2002)</name>
                        </energy_filter>
                    </specialist_optics>
                    <date>2011-06-30</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">GENERIC GATAN</film_or_detector_model>
                            <average_electron_dose_per_image units="e/&#8491;^2">80</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                    <tilt_series>
                        <axis1>
                            <min_angle units="deg">-60</min_angle>
                            <max_angle units="deg">60</max_angle>
                        </axis1>
                    </tilt_series>
                </subtomogram_averaging_microscopy>
            </microscopy_list>
            <subtomogram_averaging_processing image_processing_id="1">
                <details>Subtomogram averaging reconstruction was carried out without imposition of any symmetry.</details>
                <final_reconstruction>
                    <applied_symmetry>
                        <helical_parameters>
                            <delta_z units="&#8491;">6.3</delta_z>
                            <delta_phi units="deg">30.5</delta_phi>
                        </helical_parameters>
                    </applied_symmetry>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">36.0</resolution>
                    <resolution_method>OTHER</resolution_method>
                    <software_list>
                        <software>
                            <name>IMOD,AV3,Matlab</name>
                        </software>
                    </software_list>
                </final_reconstruction>
            </subtomogram_averaging_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="662">
        <file>emd_2043.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>65</col>
            <row>65</row>
            <sec>40</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>65</x>
            <y>65</y>
            <z>40</z>
        </spacing>
        <cell>
            <a units="&#8491;">637.0</a>
            <b units="&#8491;">637.0</b>
            <c units="&#8491;">392.0</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>-0.51170313</minimum>
            <maximum>0.45584902</maximum>
            <average>-0.00006877</average>
            <std>0.1078746</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">9.8</x>
            <y units="&#8491;">9.8</y>
            <z units="&#8491;">9.8</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.13</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Reconstruction of the Ebola virus nucleocapsid</annotation_details>
        <details>::::EMDATABANK.org::::EMD-2043::::</details>
    </map>
    <interpretation>
        <figure_list>
            <figure>
                <file>emd_2043.jpg</file>
            </figure>
        </figure_list>
    </interpretation>
</emd>