<?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_11_7/emdb.xsd" version="3.0.11.7" emdb_id="EMD-59306">
    <admin>
        <current_status>
            <date>2026-08-19</date>
            <code>REL</code>
            <processing_site>PDBe</processing_site>
        </current_status>
        <revision_history>
            <revision version="1.0" date="2026-08-19">
                <change_list>
                    <metadata>
                        <revision_type>INITIAL_RELEASE</revision_type>
                        <provider>REPOSITORY</provider>
                    </metadata>
                    <fsc>
                        <revision_type>INITIAL_RELEASE</revision_type>
                        <provider>REPOSITORY</provider>
                    </fsc>
                    <half_map part="1">
                        <revision_type>INITIAL_RELEASE</revision_type>
                        <provider>REPOSITORY</provider>
                    </half_map>
                    <half_map part="2">
                        <revision_type>INITIAL_RELEASE</revision_type>
                        <provider>REPOSITORY</provider>
                    </half_map>
                    <image>
                        <revision_type>INITIAL_RELEASE</revision_type>
                        <provider>REPOSITORY</provider>
                    </image>
                    <mask part="1">
                        <revision_type>INITIAL_RELEASE</revision_type>
                        <provider>REPOSITORY</provider>
                    </mask>
                    <primary_map>
                        <revision_type>INITIAL_RELEASE</revision_type>
                        <provider>REPOSITORY</provider>
                    </primary_map>
                </change_list>
            </revision>
        </revision_history>
        <sites>
            <deposition>PDBe</deposition>
            <last_processing>PDBe</last_processing>
        </sites>
        <key_dates>
            <deposition>2026-08-04</deposition>
            <header_release>2026-08-19</header_release>
            <map_release>2026-08-19</map_release>
            <update>2026-08-19</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>Wellcome Trust</funding_body>
                <code>311427/Z/24/Z</code>
                <country>United Kingdom</country>
            </grant_reference>
        </grant_support>
        <title>EM map of in-cell structure of the membrane-bound chloroplast ribosome in Chlamydomonas reinhardtii</title>
        <authors_list>
            <author ORCID="0000-0001-6701-144X">Hou Z</author>
            <author ORCID="0000-0003-1803-691X">Zhang P</author>
        </authors_list>
        <keywords>in-cell, chloroplast, ribosome, Chlamydomonas reinhardtii</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="false">
                    <author ORCID="0000-0001-6701-144X" order="1">Hou Z</author>
                    <author ORCID="0000-0002-0278-0771" order="2">Shen Y</author>
                    <author ORCID="0000-0001-7935-2209" order="3">Zhang Z</author>
                    <author ORCID="0000-0001-9223-774X" order="4">Lu P</author>
                    <author ORCID="0000-0003-3328-6204" order="5">Katzourakis A</author>
                    <author ORCID="0000-0003-1803-691X" order="6">Zhang P</author>
                    <title>In-cell structural analysis reveals a distinctive chloroplast ribosome in Chlamydomonas reinhardtii</title>
                    <journal_abbreviation>To Be Published</journal_abbreviation>
                    <external_references type="CSD">0353</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <other_db_list>
            <db_reference>
                <db_name>EMDB</db_name>
                <accession_id>EMD-59306</accession_id>
                <content_type>associated EM volume</content_type>
            </db_reference>
        </other_db_list>
    </crossreferences>
    <sample>
        <name>Wild-type Chlamydomonas reinhardtii cell</name>
        <supramolecule_list>
            <cell_supramolecule supramolecule_id="1">
                <name>Wild-type Chlamydomonas reinhardtii cell</name>
                <parent>0</parent>
                <natural_source database="NCBI">
                    <organism ncbi="3055">Chlamydomonas reinhardtii</organism>
                </natural_source>
            </cell_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>7.0</ph>
                    </buffer>
                    <grid>
                        <model>Quantifoil R2/1</model>
                        <material>COPPER</material>
                        <mesh>300</mesh>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">70</chamber_humidity>
                        <chamber_temperature units="K">298.15</chamber_temperature>
                        <instrument>OTHER</instrument>
                        <details>The value given for _em_vitrification.instrument is LEICA EM GP2. This is not in a list of allowed values {'SPT LABTECH CHAMELEON', 'FEI VITROBOT MARK II', 'LEICA KF80', 'EMS-002 RAPID IMMERSION FREEZER', 'LEICA EM CPC', 'GATAN CRYOPLUNGE 3', 'ZEISS PLUNGE FREEZER CRYOBOX', 'FEI VITROBOT MARK IV', 'CRYOSOL VITROJET', 'FEI VITROBOT MARK III', 'FEI VITROBOT MARK I', 'HOMEMADE PLUNGER', 'LEICA PLUNGER', 'LEICA EM GP', 'REICHERT-JUNG PLUNGER', 'SPOTITON', 'OTHER'} so OTHER is written into the XML file.</details>
                    </vitrification>
                </subtomogram_averaging_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <subtomogram_averaging_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>
                    <c2_aperture_diameter units="µm">100.0</c2_aperture_diameter>
                    <nominal_cs units="mm">2.7</nominal_cs>
                    <nominal_defocus_min units="µm">2.0</nominal_defocus_min>
                    <nominal_defocus_max units="µm">5.0</nominal_defocus_max>
                    <nominal_magnification>64000.0</nominal_magnification>
                    <specialist_optics>
                        <energy_filter>
                            <name>TFS Selectris</name>
                            <slit_width units="eV">10</slit_width>
                        </energy_filter>
                    </specialist_optics>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>TFS FALCON 4i (4k x 4k)</film_or_detector_model>
                            <average_electron_dose_per_image units="e/Å^2">2.5</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>
                    <number_classes_used>1</number_classes_used>
                    <applied_symmetry>
                        <point_group>C1</point_group>
                    </applied_symmetry>
                    <algorithm>BACK PROJECTION</algorithm>
                    <resolution units="Å" res_type="BY AUTHOR">6.9</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>4.0</version>
                        </software>
                    </software_list>
                    <number_subtomograms_used>6890</number_subtomograms_used>
                </final_reconstruction>
                <extraction>
                    <number_tomograms>260</number_tomograms>
                    <number_images_used>49911</number_images_used>
                    <software_list>
                        <software>
                            <name>emClarity</name>
                            <version>1.5.0.2</version>
                        </software>
                    </software_list>
                </extraction>
                <ctf_correction>
                    <software_list>
                        <software>
                            <name>emClarity</name>
                            <version>1.5.3.10</version>
                        </software>
                    </software_list>
                    <type>PHASE FLIPPING AND AMPLITUDE CORRECTION</type>
                </ctf_correction>
                <final_three_d_classification>
                    <number_classes>10</number_classes>
                    <average_number_members_per_class>4991.0</average_number_members_per_class>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>4.0</version>
                        </software>
                    </software_list>
                </final_three_d_classification>
                <final_angle_assignment>
                    <type>MAXIMUM LIKELIHOOD</type>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>4.0</version>
                        </software>
                    </software_list>
                </final_angle_assignment>
            </subtomogram_averaging_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="67109">
        <file>emd_59306.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">487.168</a>
            <b units="Å">487.168</b>
            <c units="Å">487.168</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>-0.39487585</minimum>
            <maximum>0.7081082</maximum>
            <average>0.0043835067</average>
            <std>0.036554005</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">1.903</x>
            <y units="Å">1.903</y>
            <z units="Å">1.903</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.119</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-59306::::</label>
    </map>
    <interpretation>
        <segmentation_list>
            <segmentation>
                <file>emd_59306_msk_1.map</file>
            </segmentation>
        </segmentation_list>
        <half_map_list>
            <half_map format="CCP4" size_kbytes="67109">
                <file>emd_59306_half_map_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>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">487.168</a>
                    <b units="Å">487.168</b>
                    <c units="Å">487.168</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>-0.5041562</minimum>
                    <maximum>0.88516945</maximum>
                    <average>0.000000000000414</average>
                    <std>0.072731026</std>
                </statistics>
                <pixel_spacing>
                    <x units="Å">1.903</x>
                    <y units="Å">1.903</y>
                    <z units="Å">1.903</z>
                </pixel_spacing>
                <contour_list>
                    <contour primary="true">
                        <source>AUTHOR</source>
                    </contour>
                </contour_list>
                <label>::::EMDATABANK.org::::EMD-59306::::</label>
            </half_map>
            <half_map format="CCP4" size_kbytes="67109">
                <file>emd_59306_half_map_2.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">487.168</a>
                    <b units="Å">487.168</b>
                    <c units="Å">487.168</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>-0.52936774</minimum>
                    <maximum>0.84736025</maximum>
                    <average>-0.000000000000305</average>
                    <std>0.073326856</std>
                </statistics>
                <pixel_spacing>
                    <x units="Å">1.903</x>
                    <y units="Å">1.903</y>
                    <z units="Å">1.903</z>
                </pixel_spacing>
                <contour_list>
                    <contour primary="true">
                        <source>AUTHOR</source>
                    </contour>
                </contour_list>
                <label>::::EMDATABANK.org::::EMD-59306::::</label>
            </half_map>
        </half_map_list>
    </interpretation>
</emd>
