<?xml version='1.0' encoding='utf-8'?>
<emd emdb_id="EMD-12699" version="3.0.2.4" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="https://github.com/emdb-empiar/emdb-schemas/blob/master/v3/v3_0_2_4/emdb.xsd">
    <admin>
        <current_status>
            <date>2021-05-26</date>
            <code>REL</code>
            <processing_site>PDBe</processing_site>
        </current_status>
        <sites>
            <deposition>PDBe</deposition>
            <last_processing>PDBe</last_processing>
        </sites>
        <key_dates>
            <deposition>2021-03-31</deposition>
            <header_release>2021-05-26</header_release>
            <map_release>2021-05-26</map_release>
            <update>2021-05-26</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>Agence Nationale de la Recherche (ANR)</funding_body>
                <code>ANR-20-CE11-0020-01</code>
                <country>France</country>
            </grant_reference>
            <grant_reference>
                <funding_body>Agence Nationale de la Recherche (ANR)</funding_body>
                <code>ANR-20-CE11-0020-03</code>
                <country>France</country>
            </grant_reference>
            <grant_reference>
                <funding_body>Agence Nationale de la Recherche (ANR)</funding_body>
                <code>ANR-19-CE11-0008-01</code>
                <country>France</country>
            </grant_reference>
            <grant_reference>
                <funding_body>German Research Foundation (DFG)</funding_body>
                <code>EL 861/1</code>
                <country>Germany</country>
            </grant_reference>
        </grant_support>
        <title>Subtomogram average of nucleosomes extracted from cryo-tomograms of Drosophila melanogaster embryos</title>
        <authors_list>
            <author>Harastani M</author>
            <author>Eltsov M</author>
            <author>Leforestier A</author>
            <author>Jonic S</author>
        </authors_list>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Harastani M</author>
                    <author order="2">Eltsov M</author>
                    <author order="3">Leforestier A</author>
                    <author order="4">Jonic S</author>
                    <title>HEMNMA-3D: Cryo Electron Tomography Method Based on Normal Mode Analysis to Study Continuous Conformational Variability of Macromolecular Complexes</title>
                    <journal_abbreviation>Front Mol Biosci</journal_abbreviation>
                    <country>CH</country>
                    <volume>8</volume>
                    <first_page>317</first_page>
                    <year>2021</year>
                    <external_references type="ISSN">2296-889X</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-12699</emdb_id>
                <relationship>
                    <other>associated EM volume</other>
                </relationship>
            </emdb_reference>
        </emdb_list>
    </crossreferences>
    <sample>
        <name>nucleosome</name>
        <supramolecule_list>
            <complex_supramolecule supramolecule_id="1">
                <name>nucleosome</name>
                <parent>0</parent>
                <natural_source database="NCBI">
                    <organism ncbi="7227">Drosophila melanogaster</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.21</theoretical>
                </molecular_weight>
            </complex_supramolecule>
        </supramolecule_list>
    </sample>
    <structure_determination_list>
        <structure_determination structure_determination_id="1">
            <method>subtomogramAveraging</method>
            <aggregation_state>cell</aggregation_state>
            <specimen_preparation_list>
                <subtomogram_averaging_preparation preparation_id="1">
                    <buffer>
                        <ph>7.5</ph>
                    </buffer>
                    <grid>
                        <model>C-flat-2/2</model>
                        <material>COPPER/PALLADIUM</material>
                        <mesh>200</mesh>
                        <support_film film_type_id="1">
                            <film_material>CARBON</film_material>
                        </support_film>
                    </grid>
                    <vitrification>
                        <cryogen_name>OTHER</cryogen_name>
                        <details>high pressure freezer HPM010 (ABRA Fluid AG). </details>
                    </vitrification>
                    <details>Drosophila melanogaster embryos were high-pressure frozen. Vitreous sections were cut with a nominal thickness of 75 nm and collected onto 200 mesh C-flat grids</details>
                </subtomogram_averaging_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <subtomogram_averaging_microscopy microscopy_id="1">
                    <microscope>FEI TITAN KRIOS</microscope>
                    <illumination_mode>OTHER</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>FIELD EMISSION GUN</electron_source>
                    <acceleration_voltage units="kV">300</acceleration_voltage>
                    <nominal_defocus_min units="µm">3.5</nominal_defocus_min>
                    <nominal_magnification>64000.0</nominal_magnification>
                    <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>GATAN K2 SUMMIT (4k x 4k)</film_or_detector_model>
                            <detector_mode>COUNTING</detector_mode>
                            <average_electron_dose_per_image units="e/Å^2">1.5</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                </subtomogram_averaging_microscopy>
            </microscopy_list>
            <subtomogram_averaging_processing image_processing_id="1">
                <image_recording_id>1</image_recording_id>
                <final_reconstruction>
                    <applied_symmetry>
                        <point_group>C1</point_group>
                    </applied_symmetry>
                    <number_subtomograms_used>600</number_subtomograms_used>
                </final_reconstruction>
                <extraction>
                    <number_tomograms>1</number_tomograms>
                    <number_images_used>667</number_images_used>
                </extraction>
                <final_three_d_classification>
                    <number_classes>1</number_classes>
                    <average_number_members_per_class>1.0</average_number_members_per_class>
                </final_three_d_classification>
                <final_angle_assignment>
                    <type>NOT APPLICABLE</type>
                </final_angle_assignment>
            </subtomogram_averaging_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="1049">
        <file>emd_12699.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>64</col>
            <row>64</row>
            <sec>64</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>64</x>
            <y>64</y>
            <z>64</z>
        </spacing>
        <cell>
            <a units="Å">281.6</a>
            <b units="Å">281.6</b>
            <c units="Å">281.6</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>-1.8754987</minimum>
            <maximum>2.7774312</maximum>
            <average>0.0044978904</average>
            <std>0.21715187</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">4.4</x>
            <y units="Å">4.4</y>
            <z units="Å">4.4</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>1.07</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-12699::::</label>
        <annotation_details>Subtomogram average of nucleosomes extracted from cryo-tomograms of vitreous sections obtained from Drosophila melanogaster embryos</annotation_details>
    </map>
</emd>