<?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_3/emdb.xsd" version="3.0.9.3" emdb_id="EMD-18876">
    <admin>
        <current_status>
            <date>2024-11-27</date>
            <code>OBS</code>
            <processing_site>PDBe</processing_site>
        </current_status>
        <sites>
            <deposition>PDBe</deposition>
            <last_processing>PDBe</last_processing>
        </sites>
        <key_dates>
            <deposition>2023-11-10</deposition>
            <header_release>2024-11-20</header_release>
            <map_release>2024-11-20</map_release>
            <obsolete>2024-11-27</obsolete>
            <update>2024-11-27</update>
        </key_dates>
        <superseded_by_list>
            <entry>
                <date>2024-11-27</date>
                <entry>EMD-52069</entry>
            </entry>
        </superseded_by_list>
        <grant_support>
            <grant_reference>
                <funding_body>German Research Foundation (DFG)</funding_body>
                <code>GRK 2566</code>
                <country>Germany</country>
            </grant_reference>
        </grant_support>
        <title>kidney slit diaphragm from mus musculus</title>
        <authors_list>
            <author>Frangakis A</author>
            <author>Birtasu A</author>
        </authors_list>
        <keywords>Slit diaphragm, Nephrin, Neph-1, cell-cell junction, MEMBRANE PROTEIN</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="false">
                    <author order="1">Frangakis A</author>
                    <author order="2">Birtasu A</author>
                    <title>kidney slit diaphragm from mus musculus</title>
                    <journal_abbreviation>To Be Published</journal_abbreviation>
                    <external_references type="CSD">0353</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>Mus musculus kidney tissue / glomerulus</name>
        <supramolecule_list>
            <tissue_supramolecule supramolecule_id="1">
                <name>Mus musculus kidney tissue / glomerulus</name>
                <parent>0</parent>
                <natural_source database="NCBI">
                    <organism ncbi="10090">Mus musculus</organism>
                    <organ>Kindey</organ>
                    <tissue>Glomerulus</tissue>
                </natural_source>
            </tissue_supramolecule>
        </supramolecule_list>
    </sample>
    <structure_determination_list>
        <structure_determination structure_determination_id="1">
            <method>tomography</method>
            <aggregation_state>tissue</aggregation_state>
            <specimen_preparation_list>
                <tomography_preparation preparation_id="1">
                    <buffer>
                        <ph>7.4</ph>
                    </buffer>
                    <vitrification>
                        <cryogen_name>NITROGEN</cryogen_name>
                    </vitrification>
                    <high_pressure_freezing>
                        <instrument>OTHER</instrument>
                        <details>The value given for _em_high_pressure_freezing.instrument is HPM 010. This is not in a list of allowed values {'EMS-002 RAPID IMMERSION FREEZER', 'LEICA EM PACT2', 'LEICA EM HPM100', 'BAL-TEC HPM 010', 'LEICA EM PACT', 'OTHER'} so OTHER is written into the XML file.</details>
                    </high_pressure_freezing>
                    <cryo_protectant>ficoll 20%</cryo_protectant>
                    <sectioning>
                        <focused_ion_beam>
                            <instrument>OTHER</instrument>
                            <ion>OTHER</ion>
                            <voltage>30</voltage>
                            <current>0.033</current>
                            <duration>3600</duration>
                            <temperature units="K">130</temperature>
                            <initial_thickness>40000</initial_thickness>
                            <final_thickness>150</final_thickness>
                            <details>The value given for _em_focused_ion_beam.instrument is FEI Helios 600i. This is not in a list of allowed values {'OTHER', 'DB235'} so OTHER is written into the XML file.</details>
                        </focused_ion_beam>
                    </sectioning>
                </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">300</acceleration_voltage>
                    <nominal_defocus_min units="µm">7.0</nominal_defocus_min>
                    <nominal_defocus_max units="µm">9.0</nominal_defocus_max>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>GATAN K2 SUMMIT (4k x 4k)</film_or_detector_model>
                            <average_electron_dose_per_image units="e/Å^2">2.38</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                </tomography_microscopy>
            </microscopy_list>
            <tomography_processing image_processing_id="1">
                <image_recording_id>1</image_recording_id>
                <final_reconstruction>
                    <algorithm>EXACT BACK PROJECTION</algorithm>
                    <number_images_used>63</number_images_used>
                </final_reconstruction>
            </tomography_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="67109">
        <file>emd_18876.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>256</col>
            <row>256</row>
            <sec>256</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>256</x>
            <y>256</y>
            <z>256</z>
        </spacing>
        <cell>
            <a units="Å">1118.208</a>
            <b units="Å">1118.208</b>
            <c units="Å">1118.208</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>-6.5329943</minimum>
            <maximum>8.090054</maximum>
            <average>-0.000000000006663</average>
            <std>0.69677645</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">4.368</x>
            <y units="Å">4.368</y>
            <z units="Å">4.368</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-18876::::</label>
    </map>
</emd>
