<entry xmlns="http://pdbe.org/empiar" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="https://ftp.ebi.ac.uk/pub/databases/emtest/empiar/schema/empiar.xsd" accessionCode="EMPIAR-12835" schemaVersion="0.65" public="true">
    <admin>
        <currentStatus>REL</currentStatus>
        <keyDates>
            <depositionDate>2025-06-09</depositionDate>
            <releaseDate>2025-08-27</releaseDate>
            <updateDate>2025-08-27</updateDate>
        </keyDates>
        <title>In-situ high-resolution cryo-EM reconstructions from CEMOVIS</title>
        <correspondingAuthor private="true">
            <authorORCID>0000-0002-9911-706X</authorORCID>
            <firstName>Johannes</firstName>
            <lastName>Elferich</lastName>
            <organization type="academic">RTI, UMass Chan Medical School, Worcester, MA</organization>
            <street>368 Plantation Street</street>
            <townOrCity>Worcester</townOrCity>
            <stateOrProvince>Massachusetts</stateOrProvince>
            <country>United States</country>
            <postOrZipCode>01655</postOrZipCode>
        </correspondingAuthor>
        <principalInvestigator private="true">
            <authorORCID>0000-0002-1506-909X</authorORCID>
            <firstName>Nikolaus</firstName>
            <lastName>Grigorieff</lastName>
            <organization type="academic">University of Massachusetts Chan Medical School</organization>
            <street>368 Plantation Street, AS4-2049</street>
            <townOrCity>Worcester</townOrCity>
            <stateOrProvince>Massachusetts</stateOrProvince>
            <country>United States</country>
            <postOrZipCode>01605</postOrZipCode>
        </principalInvestigator>
        <authorsList>
            <author authorORCID="0000-0002-9911-706X">Elferich J</author>
            <author>Kaminek M</author>
            <author authorORCID="0000-0002-5808-2649">Kong L</author>
            <author>Odriozola A</author>
            <author authorORCID="0000-0002-2778-3936">Kukulski W</author>
            <author authorORCID="0000-0001-7725-5579">Zuber B</author>
            <author authorORCID="0000-0002-1506-909X">Grigorieff N</author>
        </authorsList>
        <grantSupport>
            <grantReference>
                <fundingBody></fundingBody>
                <code></code>
                <country></country>
            </grantReference>
        </grantSupport>
        <datasetSize units="GB">573.0</datasetSize>
        <entryDOI>10.6019/EMPIAR-12835</entryDOI>
        <experimentType>EMDB</experimentType>
        <scale>cell</scale>
    </admin>
    <crossReferences>
        <relatedEMDBEntries>
            <emdbEntry>EMD-71068</emdbEntry>
        </relatedEMDBEntries>
        <citationList>
            <universalCitation>
                <journalCitation published="false" preprint="false">
                    <author authorORCID="0000-0002-9911-706X" order="1">Elferich J</author>
                    <author order="2">Kaminek M</author>
                    <author authorORCID="0000-0002-5808-2649" order="3">Kong L</author>
                    <author order="4">Odriozola A</author>
                    <author authorORCID="0000-0002-2778-3936" order="5">Kukulski W</author>
                    <author authorORCID="0000-0001-7725-5579" order="6">Zuber B</author>
                    <author authorORCID="0000-0002-1506-909X" order="7">Grigorieff N</author>
                    <title>In-situ high-resolution cryo-EM reconstructions from CEMOVIS</title>
                    <journal>International Union of Crystallography Journal</journal>
                    <journalAbbreviation>IUCrJ</journalAbbreviation>
                    <country>United Kingdom</country>
                    <year>2025</year>
                    <details>933 micrographs of CEMOVIS sections of Saccharomyces cerevisiae cells that were searched using 2D template matching, using the mature Saccharomyces cerevisiae 60S ribosomal subunit as templates. The 60S template contained omitted regions of density that was present in the reconstruction from the detected targets (EMD-71068).</details>
                </journalCitation>
            </universalCitation>
            <universalCitation>
                <journalCitation published="true" preprint="true">
                    <author authorORCID="0000-0002-9911-706X" order="1">Elferich J</author>
                    <author order="2">Kaminek M</author>
                    <author authorORCID="0000-0002-5808-2649" order="3">Kong L</author>
                    <author order="4">Odriozola A</author>
                    <author authorORCID="0000-0002-2778-3936" order="5">Kukulski W</author>
                    <author authorORCID="0000-0001-7725-5579" order="6">Zuber B</author>
                    <author authorORCID="0000-0002-1506-909X" order="7">Grigorieff N</author>
                    <title>In-situ high-resolution cryo-EM reconstructions from CEMOVIS</title>
                    <journal>bioRxiv</journal>
                    <journalAbbreviation></journalAbbreviation>
                    <country></country>
                    <year>2025</year>
                    <externalReferences type="doi">10.1101/2025.03.29.646093</externalReferences>
                    <details>307 micrographs of CEMOVIS sections of Saccharomyces cerevisiae cells that were searched using 2D template matching, using the mature Saccharomyces cerevisiae 60S ribosomal subunit as templates. The 60S template contained omitted regions of density that was present in the reconstruction from the detected targets (EMD-71068).</details>
                </journalCitation>
            </universalCitation>
        </citationList>
    </crossReferences>
    <imageSet>
        <name>Unaligned multi-frame microgaphs of yeast cells sectioned using CEMOVIS</name>
        <directory>/data/micrographs</directory>
        <category>micrographs - multiframe</category>
        <headerFormat>EER</headerFormat>
        <dataFormat>EER</dataFormat>
        <numImagesOrTiltSeries>933</numImagesOrTiltSeries>
        <framesPerImage>1863</framesPerImage>
        <voxelType>SIGNED BYTE</voxelType>
        <dimensions>
            <imageWidth>16384</imageWidth>
            <pixelWidth>0.2925</pixelWidth>
            <imageHeight>16384</imageHeight>
            <pixelHeight>0.2925</pixelHeight>
        </dimensions>
        <details></details>
        <segmentationList/>
        <micrographsFilePattern></micrographsFilePattern>
        <pickedParticlesFilePattern></pickedParticlesFilePattern>
        <pickedParticlesDirectory></pickedParticlesDirectory>
    </imageSet>
    <imageSet>
        <name>Aligned single-frame microgaphs of yeast cells sectioned using CEMOVIS</name>
        <directory>/data/micrographs</directory>
        <category>micrographs - single frame</category>
        <headerFormat>MRC</headerFormat>
        <dataFormat>MRC</dataFormat>
        <numImagesOrTiltSeries>933</numImagesOrTiltSeries>
        <framesPerImage>1</framesPerImage>
        <voxelType>32 BIT FLOAT</voxelType>
        <dimensions>
            <imageWidth>4096</imageWidth>
            <pixelWidth>1.17</pixelWidth>
            <imageHeight>4096</imageHeight>
            <pixelHeight>1.17</pixelHeight>
        </dimensions>
        <details>Particle positions and orientations derived from 2DTM are stored in cisTEM star format.</details>
        <segmentationList/>
        <micrographsFilePattern></micrographsFilePattern>
        <pickedParticlesFilePattern>data/2dtm_results/*.star</pickedParticlesFilePattern>
        <pickedParticlesDirectory>data/2dtm_results</pickedParticlesDirectory>
    </imageSet>
    <imageSet>
        <name>Template used for 2DTM with omitted regions</name>
        <directory>/data/template</directory>
        <category>reconstructed volumes</category>
        <headerFormat>MRC</headerFormat>
        <dataFormat>MRC</dataFormat>
        <numImagesOrTiltSeries>1</numImagesOrTiltSeries>
        <framesPerImage>1</framesPerImage>
        <voxelType>32 BIT FLOAT</voxelType>
        <dimensions>
            <imageWidth>512</imageWidth>
            <pixelWidth>variable</pixelWidth>
            <imageHeight>512</imageHeight>
            <pixelHeight>variable</pixelHeight>
        </dimensions>
        <details></details>
        <segmentationList/>
        <micrographsFilePattern></micrographsFilePattern>
        <pickedParticlesFilePattern></pickedParticlesFilePattern>
        <pickedParticlesDirectory></pickedParticlesDirectory>
    </imageSet>
</entry>
