<emd emdb_id="EMD-2489" 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>2013-10-18</deposition>
            <header_release>2013-11-13</header_release>
            <map_release>2013-11-13</map_release>
            <update>2013-12-11</update>
        </key_dates>
        <title>Determination of protein structure at 8.5 Angstrom resolution using cryo-electron microscopy and subtomogram averaging</title>
        <authors_list>
            <author>Schur FKM</author>
            <author>Hagen W</author>
            <author>de Marco A</author>
            <author>Briggs JAG</author>
        </authors_list>
        <keywords>Cryo-electron Tomography, Sub-tomogram Averaging, Retrovirus, Capsid</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Schur FKM</author>
                    <author order="2">Hagen W</author>
                    <author order="3">de Marco A</author>
                    <author order="4">Briggs JAG</author>
                    <title>Determination of protein structure at 8.5 Angstrom resolution using cryo-electron microscopy and subtomogram averaging</title>
                    <journal>J.STRUCT.BIOL.</journal>
                    <volume>184</volume>
                    <first_page>394</first_page>
                    <last_page>400</last_page>
                    <year>2013</year>
                    <external_references type="PUBMED">24184468</external_references>
                    <external_references type="DOI">doi:10.1016/j.jsb.2013.10.015</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>M-MPV CANC Gag lattice</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>M-MPV CANC Gag lattice</name>
                <oligomeric_state>helical</oligomeric_state>
                <number_unique_components>1</number_unique_components>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>M-MPV dPro CANC protein</name>
                <natural_source database="NCBI">
                    <organism ncbi="11855">Mason-Pfizer monkey virus</organism>
                </natural_source>
                <oligomeric_state>helical</oligomeric_state>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                </recombinant_expression>
                <sequence />
            </protein_or_peptide>
        </macromolecule_list>
    </sample>
    <structure_determination_list>
        <structure_determination structure_determination_id="1">
            <method>tomography</method>
            <aggregation_state>helicalArray</aggregation_state>
            <specimen_preparation_list>
                <tomography_preparation preparation_id="1">
                    <buffer>
                        <ph>7.7</ph>
                        <details>50mM Tris, 100mM NaCl,1uM Zn</details>
                    </buffer>
                    <grid>
                        <details>300mesh copper, glow discharged</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <instrument>OTHER</instrument>
                    </vitrification>
                </tomography_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <tomography_microscopy microscopy_id="1">
                    <microscope>FEI TITAN KRIOS</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_cs units="mm">2.7</nominal_cs>
                    <nominal_defocus_min units="&#181;m">3.3</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">3.3</nominal_defocus_max>
                    <nominal_magnification>42000.0</nominal_magnification>
                    <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
                    <specialist_optics>
                        <energy_filter>
                            <name>GIF2002 postcolumn energy filter</name>
                        </energy_filter>
                    </specialist_optics>
                    <date>2013-05-21</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">GENERIC GATAN (2k x 2k)</film_or_detector_model>
                            <number_real_images>36</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">40</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                    <specimen_holder>Liquid nitrogen cooled</specimen_holder>
                    <tilt_series>
                        <axis1>
                            <min_angle units="deg">-45</min_angle>
                            <max_angle units="deg">60</max_angle>
                            <angle_increment units="deg">3</angle_increment>
                        </axis1>
                    </tilt_series>
                </tomography_microscopy>
            </microscopy_list>
            <tomography_processing image_processing_id="1">
                <details>Tilt series was reconstructed using IMOD</details>
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <software_list>
                        <software>
                            <name>IMOD</name>
                        </software>
                    </software_list>
                    <number_images_used>36</number_images_used>
                </final_reconstruction>
            </tomography_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="5701633">
        <file>emd_2489.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS SIGNED INTEGER (2 BYTES)</data_type>
        <dimensions>
            <col>2048</col>
            <row>2048</row>
            <sec>696</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>42</sec>
        </origin>
        <spacing>
            <x>2048</x>
            <y>2048</y>
            <z>696</z>
        </spacing>
        <cell>
            <a units="&#8491;">4147.2</a>
            <b units="&#8491;">4147.2</b>
            <c units="&#8491;">1409.4</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>-32767.0</minimum>
            <maximum>23112.0</maximum>
            <average>133.224792479999991</average>
            <std>3780.626953129999947</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">2.025</x>
            <y units="&#8491;">2.025</y>
            <z units="&#8491;">2.025</z>
        </pixel_spacing>
        <annotation_details>Tomogram reconstruction of a tilt-series containing M-MPMV dPro CANC tubes</annotation_details>
        <details>::::EMDATABANK.org::::EMD-2489::::</details>
    </map>
    <interpretation>
        <figure_list>
            <figure>
                <file>emd_2489.tif</file>
            </figure>
        </figure_list>
    </interpretation>
</emd>