<?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-51424">
    <admin>
        <current_status>
            <date>2024-10-30</date>
            <code>REL</code>
            <processing_site>PDBe</processing_site>
        </current_status>
        <sites>
            <deposition>PDBe</deposition>
            <last_processing>PDBe</last_processing>
        </sites>
        <key_dates>
            <deposition>2024-08-25</deposition>
            <header_release>2024-10-09</header_release>
            <map_release>2024-10-09</map_release>
            <update>2024-10-30</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>European Research Council (ERC)</funding_body>
                <code>M822.00045</code>
                <country>European Union</country>
            </grant_reference>
        </grant_support>
        <title>Tomogram of pyrenoid of T. pseudonana Shell4 knock-out</title>
        <authors_list>
            <author>Demulder M</author>
            <author>Engel B</author>
        </authors_list>
        <keywords>pyrenoid, rubisco, protein shell, carbon fixation, chloroplast, marine diatom, PHOTOSYNTHESIS</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Nam O</author>
                    <author order="2">Musial S</author>
                    <author order="3">Demulder M</author>
                    <author order="4">McKenzie C</author>
                    <author order="5">Dowle A</author>
                    <author order="6">Dowson M</author>
                    <author order="7">Barrett J</author>
                    <author order="8">Blaza JN</author>
                    <author order="9">Engel BD</author>
                    <author order="10">Mackinder LCM</author>
                    <title>A protein blueprint of the diatom CO 2 -fixing organelle.</title>
                    <journal_abbreviation>Cell</journal_abbreviation>
                    <volume>187</volume>
                    <first_page>5935</first_page>
                    <last_page>5950.e18</last_page>
                    <year>2024</year>
                    <external_references type="PUBMED">39368476</external_references>
                    <external_references type="DOI">doi:10.1016/j.cell.2024.09.025</external_references>
                    <external_references type="ISSN">1097-4172</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>T. pseudonana shell4 KO</name>
        <supramolecule_list>
            <cell_supramolecule supramolecule_id="1">
                <name>T. pseudonana shell4 KO</name>
                <parent>0</parent>
                <natural_source database="NCBI">
                    <organism ncbi="35128">T. pseudonana</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>7.5</ph>
                    </buffer>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <instrument>FEI VITROBOT MARK II</instrument>
                    </vitrification>
                    <sectioning>
                        <focused_ion_beam>
                            <instrument>OTHER</instrument>
                            <ion>OTHER</ion>
                            <voltage>30</voltage>
                            <current>20</current>
                            <duration>1</duration>
                            <temperature units="K">93</temperature>
                            <initial_thickness>1000</initial_thickness>
                            <final_thickness>150</final_thickness>
                            <details>The value given for _em_focused_ion_beam.instrument is Aquilos 2. 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>TFS 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">0.003</nominal_defocus_min>
                    <nominal_defocus_max units="µm">0.003</nominal_defocus_max>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>GATAN K3 BIOQUANTUM (6k x 4k)</film_or_detector_model>
                            <average_electron_dose_per_image units="e/Å^2">2.0</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>45</number_images_used>
                </final_reconstruction>
            </tomography_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="754975">
        <file>emd_51424.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS SIGNED BYTE</data_type>
        <dimensions>
            <col>1024</col>
            <row>1440</row>
            <sec>512</sec>
        </dimensions>
        <origin>
            <col>261</col>
            <row>-261</row>
            <sec>-321</sec>
        </origin>
        <spacing>
            <x>1024</x>
            <y>1440</y>
            <z>512</z>
        </spacing>
        <cell>
            <a units="Å">10997.76</a>
            <b units="Å">15465.6</b>
            <c units="Å">5498.88</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>-112.0</minimum>
            <maximum>106.0</maximum>
            <average>-1.0000427</average>
            <std>10.004167000000001</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">10.74</x>
            <y units="Å">10.74</y>
            <z units="Å">10.74</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-51424::::</label>
    </map>
    <interpretation>
        <additional_map_list>
            <additional_map format="CCP4" size_kbytes="3019899">
                <file>emd_51424_additional_1.map.gz</file>
                <symmetry>
                    <space_group>1</space_group>
                </symmetry>
                <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
                <dimensions>
                    <col>1024</col>
                    <row>1440</row>
                    <sec>512</sec>
                </dimensions>
                <origin>
                    <col>208</col>
                    <row>-208</row>
                    <sec>-256</sec>
                </origin>
                <spacing>
                    <x>1024</x>
                    <y>1440</y>
                    <z>512</z>
                </spacing>
                <cell>
                    <a units="Å">10997.76</a>
                    <b units="Å">15465.6</b>
                    <c units="Å">5498.88</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>-0.7822621</minimum>
                    <maximum>0.86028993</maximum>
                    <average>0.01202275</average>
                    <std>0.10823417</std>
                </statistics>
                <pixel_spacing>
                    <x units="Å">10.74</x>
                    <y units="Å">10.74</y>
                    <z units="Å">10.74</z>
                </pixel_spacing>
                <contour_list>
                    <contour primary="true">
                        <source>AUTHOR</source>
                    </contour>
                </contour_list>
                <label>::::EMDATABANK.org::::EMD-51424::::</label>
            </additional_map>
        </additional_map_list>
    </interpretation>
</emd>
