<?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-18231">
    <admin>
        <current_status>
            <date>2024-08-21</date>
            <code>REL</code>
            <processing_site>PDBe</processing_site>
        </current_status>
        <sites>
            <deposition>PDBe</deposition>
            <last_processing>PDBe</last_processing>
        </sites>
        <key_dates>
            <deposition>2023-08-16</deposition>
            <header_release>2023-08-30</header_release>
            <map_release>2023-08-30</map_release>
            <update>2024-08-21</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>Max Planck Society</funding_body>
                <country>Germany</country>
            </grant_reference>
            <grant_reference>
                <funding_body>Other private</funding_body>
            </grant_reference>
        </grant_support>
        <title>CryoDRGN Reconstruction of 80S Ribosome in Rotated State from S.cerevisiae Prepared using Cryo-plasmaFIB Milling</title>
        <authors_list>
            <author>Rangan R</author>
            <author ORCID="0000-0003-2020-3561">Khavnekar S</author>
            <author>Lerer A</author>
            <author>Johnston J</author>
            <author>Kelley R</author>
            <author>Obr M</author>
            <author ORCID="0000-0002-4480-5439">Kotecha A</author>
            <author>Zhong ED</author>
        </authors_list>
        <keywords>yeast 80S, RIBOSOME</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Rangan R</author>
                    <author order="2">Feathers R</author>
                    <author order="3">Khavnekar S</author>
                    <author ORCID="0000-0002-5216-6542" order="4">Lerer A</author>
                    <author order="5">Johnston JD</author>
                    <author order="6">Kelley R</author>
                    <author ORCID="0000-0003-1756-6564" order="7">Obr M</author>
                    <author ORCID="0000-0002-4480-5439" order="8">Kotecha A</author>
                    <author ORCID="0000-0001-6345-1907" order="9">Zhong ED</author>
                    <title>CryoDRGN-ET: deep reconstructing generative networks for visualizing dynamic biomolecules inside cells.</title>
                    <journal_abbreviation>Nat.Methods</journal_abbreviation>
                    <country>US</country>
                    <volume>21</volume>
                    <first_page>1537</first_page>
                    <last_page>1545</last_page>
                    <year>2024</year>
                    <external_references type="PUBMED">39025970</external_references>
                    <external_references type="DOI">doi:10.1038/s41592-024-02340-4</external_references>
                    <external_references type="ISSN">1548-7105</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>80S S. cerevisiae</name>
        <supramolecule_list>
            <complex_supramolecule supramolecule_id="1">
                <name>80S S. cerevisiae</name>
                <parent>0</parent>
                <natural_source database="NCBI">
                    <organism ncbi="4932">Saccharomyces cerevisiae</organism>
                </natural_source>
            </complex_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>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                    </vitrification>
                </subtomogram_averaging_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <subtomogram_averaging_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">1.0</nominal_defocus_min>
                    <nominal_defocus_max units="µm">3.5</nominal_defocus_max>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>FEI FALCON IV (4k x 4k)</film_or_detector_model>
                            <average_electron_dose_per_image units="e/Å^2">3.5</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>
                    <applied_symmetry>
                        <point_group>C1</point_group>
                    </applied_symmetry>
                    <resolution units="Å" res_type="BY AUTHOR">4.7</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>cryoDRGN</name>
                            <processing_details>Electron Tomography</processing_details>
                        </software>
                    </software_list>
                    <number_subtomograms_used>62624</number_subtomograms_used>
                </final_reconstruction>
                <extraction>
                    <number_tomograms>250</number_tomograms>
                    <number_images_used>250000</number_images_used>
                </extraction>
                <final_angle_assignment>
                    <type>OTHER</type>
                </final_angle_assignment>
            </subtomogram_averaging_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="67109">
        <file>emd_18231.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">501.76</a>
            <b units="Å">501.76</b>
            <c units="Å">501.76</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>-0.039299782</minimum>
            <maximum>0.08681587</maximum>
            <average>0.000000000360709</average>
            <std>0.004951836</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">1.96</x>
            <y units="Å">1.96</y>
            <z units="Å">1.96</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.017</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-18231::::</label>
        <annotation_details>TOMOMAN-STOPGAP-Warp-Relion-M
CryoDRGN-ET rotated 80S yeast</annotation_details>
    </map>
    <interpretation>
        <segmentation_list>
            <segmentation>
                <file>emd_18231_msk_1.map</file>
            </segmentation>
        </segmentation_list>
        <half_map_list>
            <half_map format="CCP4" size_kbytes="67109">
                <file>emd_18231_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">501.76</a>
                    <b units="Å">501.76</b>
                    <c units="Å">501.76</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>-0.018595837</minimum>
                    <maximum>0.05276675</maximum>
                    <average>0.00000000036305</average>
                    <std>0.0034526929</std>
                </statistics>
                <pixel_spacing>
                    <x units="Å">1.96</x>
                    <y units="Å">1.96</y>
                    <z units="Å">1.96</z>
                </pixel_spacing>
                <contour_list>
                    <contour primary="true">
                        <source>AUTHOR</source>
                    </contour>
                </contour_list>
                <label>::::EMDATABANK.org::::EMD-18231::::</label>
                <annotation_details>TOMOMAN-STOPGAP-Warp-Relion-M
CryoDRGN-ET rotated 80S yeast</annotation_details>
            </half_map>
            <half_map format="CCP4" size_kbytes="67109">
                <file>emd_18231_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">501.76</a>
                    <b units="Å">501.76</b>
                    <c units="Å">501.76</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>-0.018020036</minimum>
                    <maximum>0.05494542</maximum>
                    <average>0.000000000358294</average>
                    <std>0.003462235</std>
                </statistics>
                <pixel_spacing>
                    <x units="Å">1.96</x>
                    <y units="Å">1.96</y>
                    <z units="Å">1.96</z>
                </pixel_spacing>
                <contour_list>
                    <contour primary="true">
                        <source>AUTHOR</source>
                    </contour>
                </contour_list>
                <label>::::EMDATABANK.org::::EMD-18231::::</label>
                <annotation_details>TOMOMAN-STOPGAP-Warp-Relion-M
CryoDRGN-ET rotated 80S yeast</annotation_details>
            </half_map>
        </half_map_list>
    </interpretation>
</emd>
