<?xml version="1.0" encoding="UTF-8"?>
<emd emdb_id="EMD-35098">
    <admin>
        <current_status>
            <date>2023-06-07</date>
            <code>REL</code>
            <processing_site>PDBj</processing_site>
        </current_status>
        <sites>
            <deposition>PDBj</deposition>
            <last_processing>PDBj</last_processing>
        </sites>
        <key_dates>
            <deposition>2023-01-10</deposition>
            <header_release>2023-03-08</header_release>
            <map_release>2023-03-08</map_release>
            <update>2023-06-07</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>Not funded</funding_body>
            </grant_reference>
        </grant_support>
        <title>Tomogram of daughter buds in mature Toxoplasma gondii tachyzoite</title>
        <authors_list>
            <author>Li Z</author>
            <author>Guo Q</author>
        </authors_list>
        <keywords>Toxoplasma, daughter buds, conoid, tachyzoite, CELL INVASION</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Li Z</author>
                    <author order="2">Du W</author>
                    <author order="3">Yang J</author>
                    <author order="4">Lai DH</author>
                    <author order="5">Lun ZR</author>
                    <author ORCID="0000-0003-3520-5439" order="6">Guo Q</author>
                    <title>Cryo-Electron Tomography of Toxoplasma gondii Indicates That the Conoid Fiber May Be Derived from Microtubules.</title>
                    <journal_abbreviation>Adv Sci</journal_abbreviation>
                    <country>DE</country>
                    <volume>10</volume>
                    <first_page>e2206595</first_page>
                    <last_page>e2206595</last_page>
                    <year>2023</year>
                    <external_references type="PUBMED">36840635</external_references>
                    <external_references type="DOI">doi:10.1002/advs.202206595</external_references>
                    <external_references type="ISSN">2198-3844</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-35098</emdb_id>
                <relationship>
                    <other>associated EM volume</other>
                </relationship>
            </emdb_reference>
        </emdb_list>
    </crossreferences>
    <sample>
        <name>Daughter buds in tachyzoite</name>
        <supramolecule_list>
            <cell_supramolecule supramolecule_id="1">
                <name>Daughter buds in tachyzoite</name>
                <parent>0</parent>
                <natural_source database="NCBI">
                    <organism ncbi="383379">Toxoplasma gondii RH</organism>
                </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>7.0</ph>
                    </buffer>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                    </vitrification>
                    <sectioning>
                        <focused_ion_beam>
                            <instrument>OTHER</instrument>
                            <ion>OTHER</ion>
                            <voltage>30</voltage>
                            <current>0.5</current>
                            <duration>1800</duration>
                            <temperature units="K">100</temperature>
                            <initial_thickness>1000</initial_thickness>
                            <final_thickness>180</final_thickness>
                            <details>The value given for _em_focused_ion_beam.instrument is Aquilos. 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">3.0</nominal_defocus_min>
                    <nominal_defocus_max units="µm">5.0</nominal_defocus_max>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>GATAN K3 (6k x 4k)</film_or_detector_model>
                            <average_electron_dose_per_image units="e/Å^2">3.0</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>
                    <number_images_used>38</number_images_used>
                </final_reconstruction>
            </tomography_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="258049">
        <file>emd_35098.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>512</col>
            <row>720</row>
            <sec>175</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>512</x>
            <y>720</y>
            <z>175</z>
        </spacing>
        <cell>
            <a units="Å">13631.488</a>
            <b units="Å">19169.281</b>
            <c units="Å">4659.2</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>-6.6005325</minimum>
            <maximum>3.02679</maximum>
            <average>-0.000000000058191</average>
            <std>0.30327895</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">26.624</x>
            <y units="Å">26.624002</y>
            <z units="Å">26.624</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-35098::::</label>
    </map>
</emd>
