<?xml version="1.0" encoding="UTF-8"?>
<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="https://ftp.ebi.ac.uk/pub/databases/em_ebi/emdb_related/emdb-schemas/emdb_schemas/v3/v3_0_9_0/emdb.xsd" version="3.0.9.0" emdb_id="EMD-15061">
    <admin>
        <current_status>
            <date>2023-12-13</date>
            <code>REL</code>
            <processing_site>PDBe</processing_site>
        </current_status>
        <sites>
            <deposition>PDBe</deposition>
            <last_processing>PDBe</last_processing>
        </sites>
        <key_dates>
            <deposition>2022-05-30</deposition>
            <header_release>2022-07-06</header_release>
            <map_release>2022-07-06</map_release>
            <update>2023-12-13</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>Israel Science Foundation</funding_body>
                <code>1696/18</code>
                <country>Israel</country>
            </grant_reference>
        </grant_support>
        <title>Fibroblast nucleus sub-volume.</title>
        <authors_list>
            <author ORCID="0000-0001-6285-0228">Sedat J</author>
            <author ORCID="0000-0003-0454-3208">McDonald A</author>
            <author ORCID="0000-0001-7915-5512">Elbaum M</author>
        </authors_list>
        <keywords>nucleus, chromatin, STEM, DNA</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Sedat J</author>
                    <author order="2">McDonald A</author>
                    <author order="3">Cang H</author>
                    <author order="4">Lucas J</author>
                    <author order="5">Arigovindan M</author>
                    <author order="6">Kam Z</author>
                    <author order="7">Murre C</author>
                    <author ORCID="0000-0001-7915-5512" order="8">Elbaum M</author>
                    <title>A proposed unified interphase nucleus chromosome structure: Preliminary preponderance of evidence.</title>
                    <journal_abbreviation>Proc.Natl.Acad.Sci.USA</journal_abbreviation>
                    <country>US</country>
                    <volume>119</volume>
                    <first_page>e2119101119</first_page>
                    <last_page>e2119101119</last_page>
                    <year>2022</year>
                    <external_references type="PUBMED">35749363</external_references>
                    <external_references type="DOI">doi:10.1073/pnas.2119101119</external_references>
                    <external_references type="ISSN">1091-6490</external_references>
                    <external_references type="CSD">0040</external_references>
                    <external_references type="ASTM">PNASA6</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-14924</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
                <details>sub-volume used for stereo movie (RASP) in publication</details>
            </emdb_reference>
        </emdb_list>
    </crossreferences>
    <sample>
        <name>WI-38 fibroblast cell</name>
        <supramolecule_list>
            <cell_supramolecule supramolecule_id="1">
                <name>WI-38 fibroblast cell</name>
                <parent>0</parent>
                <details>cells cultured directly on gold EM grid</details>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                    <organ>lung</organ>
                    <tissue>cell culture</tissue>
                </natural_source>
            </cell_supramolecule>
        </supramolecule_list>
    </sample>
    <structure_determination_list>
        <structure_determination structure_determination_id="1">
            <method>tomography</method>
            <aggregation_state>cell</aggregation_state>
            <specimen_preparation_list>
                <tomography_preparation preparation_id="1">
                    <buffer>
                        <ph>7.4</ph>
                        <details>Minimal Essential Medium (Gibco) supplemented with 15% fetal calf serum, L-glutamine, and penicillin/streptomycin.</details>
                    </buffer>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <instrument>LEICA EM GP</instrument>
                    </vitrification>
                    <details>WI-38 embryonic lung fibroblast cells (obtained from Coriell Institute) were cultured directly on gold EM grids and imaged intact by cryo-STEM tomography (CSTET).</details>
                    <fiducial_markers_list>
                        <fiducial_marker>
                            <manufacturer>obtained from L Duchesne (https://doi.org/10.1021/la802876u )</manufacturer>
                            <diameter units="nanometer">10</diameter>
                        </fiducial_marker>
                    </fiducial_markers_list>
                    <sectioning>
                        <other_sectioning>NO SECTIONING</other_sectioning>
                    </sectioning>
                </tomography_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <tomography_microscopy microscopy_id="1">
                    <microscope>FEI TECNAI F20</microscope>
                    <illumination_mode>SPOT SCAN</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>FIELD EMISSION GUN</electron_source>
                    <acceleration_voltage units="kV">200</acceleration_voltage>
                    <c2_aperture_diameter units="µm">20.0</c2_aperture_diameter>
                    <nominal_cs units="mm">2.0</nominal_cs>
                    <nominal_defocus_min units="µm">0.0</nominal_defocus_min>
                    <nominal_defocus_max units="µm">0.0</nominal_defocus_max>
                    <specimen_holder_model>GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER</specimen_holder_model>
                    <cooling_holder_cryogen>NITROGEN</cooling_holder_cryogen>
                    <alignment_procedure>
                        <other/>
                    </alignment_procedure>
                    <specialist_optics>
                        <details>STEM data collection in BF mode.</details>
                    </specialist_optics>
                    <details>NanoProbe STEM acquisition.</details>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>OTHER</film_or_detector_model>
                            <digitization_details>
                                <dimensions>
                                    <width units="pixel">2048</width>
                                    <height units="pixel">2048</height>
                                </dimensions>
                            </digitization_details>
                            <number_grids_imaged>1</number_grids_imaged>
                            <number_real_images>61</number_real_images>
                            <average_exposure_time units="s">12.6</average_exposure_time>
                            <average_electron_dose_per_image units="e/Å^2">3.8</average_electron_dose_per_image>
                            <details>Cryo-STEM tilt series</details>
                        </image_recording>
                    </image_recording_list>
                </tomography_microscopy>
            </microscopy_list>
            <tomography_processing image_processing_id="1">
                <image_recording_id>1</image_recording_id>
                <details>Gatan STEM BF/ADF detector</details>
                <final_reconstruction>
                    <algorithm>BACK PROJECTION</algorithm>
                    <software_list>
                        <software>
                            <name>TOMO3D</name>
                        </software>
                        <software>
                            <name>PRIISM/IVE</name>
                        </software>
                    </software_list>
                    <number_images_used>56</number_images_used>
                </final_reconstruction>
            </tomography_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="66929">
        <file>emd_15061.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>356</col>
            <row>470</row>
            <sec>100</sec>
        </dimensions>
        <origin>
            <col>40</col>
            <row>180</row>
            <sec>187</sec>
        </origin>
        <spacing>
            <x>356</x>
            <y>470</y>
            <z>100</z>
        </spacing>
        <cell>
            <a units="Å">11926.0</a>
            <b units="Å">15745.0</b>
            <c units="Å">3350.0</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>1500.0</minimum>
            <maximum>3073.685500000000047</maximum>
            <average>1679.505000000000109</average>
            <std>171.782000000000011</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">33.5</x>
            <y units="Å">33.5</y>
            <z units="Å">33.5</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-15061::::</label>
        <annotation_details>sub-volume of EMD-14924. corresponds to Supplementary Movie S6.</annotation_details>
    </map>
</emd>
