<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-10640" schemaVersion="0.65" public="true">
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        <keyDates>
            <depositionDate>2021-02-11</depositionDate>
            <releaseDate>2021-03-05</releaseDate>
            <updateDate>2021-03-05</updateDate>
        </keyDates>
        <title>Cryo-EM of Multiple System Atrophy seeded assembly of alpha-synuclein filaments</title>
        <correspondingAuthor private="true">
            <authorORCID>0000-0002-2152-1476</authorORCID>
            <firstName>Sofia</firstName>
            <middleName>Karin Anna</middleName>
            <lastName>Lövestam</lastName>
            <organization type="academic">MRC LMB Cambridge</organization>
            <street>Francis Crick Avenue</street>
            <townOrCity>Cambridge</townOrCity>
            <stateOrProvince>Cambridgeshire</stateOrProvince>
            <country>United Kingdom</country>
            <postOrZipCode>CB2 0QH</postOrZipCode>
        </correspondingAuthor>
        <principalInvestigator private="true">
            <authorORCID>0000-0002-0462-6540</authorORCID>
            <firstName>Sjors</firstName>
            <lastName>Scheres</lastName>
            <organization type="academic">MRC LMB Cambridge</organization>
            <street>Francis Crick Avenue</street>
            <townOrCity>Cambridge</townOrCity>
            <stateOrProvince>Cambridgeshire</stateOrProvince>
            <country>United Kingdom</country>
            <postOrZipCode>CB2 0QH</postOrZipCode>
        </principalInvestigator>
        <authorsList>
            <author authorORCID="0000-0002-2152-1476">Lövestam S</author>
            <author authorORCID="0000-0002-5214-7886">Goedert M</author>
            <author authorORCID="0000-0002-0462-6540">Scheres S</author>
        </authorsList>
        <datasetSize units="TB">1.1</datasetSize>
        <entryDOI>10.6019/EMPIAR-10640</entryDOI>
        <experimentType>EMDB</experimentType>
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    <crossReferences>
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            <emdbEntry>EMD-12264</emdbEntry>
            <emdbEntry>EMD-12265</emdbEntry>
            <emdbEntry>EMD-12266</emdbEntry>
            <emdbEntry>EMD-12267</emdbEntry>
            <emdbEntry>EMD-12268</emdbEntry>
            <emdbEntry>EMD-12269</emdbEntry>
        </relatedEMDBEntries>
        <citationList>
            <universalCitation>
                <journalCitation published="true" preprint="false">
                    <author authorORCID="0000-0002-2152-1476" order="1">Lövestam S</author>
                    <author authorORCID="0000-0002-1848-1610" order="2">Schweighauser M</author>
                    <author authorORCID="0000-0002-7559-8284" order="3">Matsubara T</author>
                    <author authorORCID="0000-0001-9709-5242" order="4">Murayama S</author>
                    <author authorORCID="0000-0002-0075-5943" order="5">Tomita T</author>
                    <author authorORCID="0000-0001-7045-7098" order="6">Ando T</author>
                    <author authorORCID="0000-0002-0142-4839" order="7">Hasegawa K</author>
                    <author authorORCID="0000-0002-8520-6184" order="8">Yoshida M</author>
                    <author authorORCID="0000-0003-3835-9070" order="9">Tarutani A</author>
                    <author authorORCID="0000-0001-7415-8159" order="10">Hasegawa M</author>
                    <author authorORCID="0000-0002-5214-7886" order="11">Goedert M</author>
                    <author authorORCID="0000-0002-0462-6540" order="12">Scheres S</author>
                    <title>Seeded assembly in vitro does not replicate the structures of α-synuclein filaments from multiple system atrophy</title>
                    <journal>FEBS Open Bio</journal>
                    <journalAbbreviation>FEBS Open Bio</journalAbbreviation>
                    <country>United Kingdom</country>
                    <year>2021</year>
                    <language>English</language>
                    <externalReferences type="doi">10.1002/2211-5463.13110</externalReferences>
                    <externalReferences type="pubmed">33548114</externalReferences>
                </journalCitation>
            </universalCitation>
        </citationList>
    </crossReferences>
    <imageSet>
        <name>Unaligned movies of alpha-synuclein filament seeded in vitro by filaments purified from Multiple Systems Atrophy Case 1</name>
        <directory>/data/EMPIAR_upload/Movies/Case1</directory>
        <category>micrographs - multiframe</category>
        <headerFormat>TIFF</headerFormat>
        <dataFormat>TIFF</dataFormat>
        <numImagesOrTiltSeries>2175</numImagesOrTiltSeries>
        <framesPerImage>40</framesPerImage>
        <frameRange>
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        <dimensions>
            <imageWidth>3838</imageWidth>
            <pixelWidth>1.1</pixelWidth>
            <imageHeight>3710</imageHeight>
            <pixelHeight>1.1</pixelHeight>
        </dimensions>
        <details>Unaligned and non-gain corrected, 40-frame movies (K2 counting mode) were collected with EPU using a Titan Krios operating at 300 kV (LMB Krios II). The exposure was at  36.7 e/A^2) with a defocus range of -2.8 to -1.5 um. Micrographs were manually picked in relion using start-end helical picking. Gain reference is in Movies/Case1-gain-ref.MRC. Have fun.</details>
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        <name>Unaligned movies of alpha-synuclein filament seeded in vitro by filaments purified from Multiple Systems Atrophy Case 2</name>
        <directory>/data/EMPIAR_upload/Movies/Case2</directory>
        <category>micrographs - multiframe</category>
        <headerFormat>TIFF</headerFormat>
        <dataFormat>TIFF</dataFormat>
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        <framesPerImage>40</framesPerImage>
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            <imageHeight>3710</imageHeight>
            <pixelHeight>1.14</pixelHeight>
        </dimensions>
        <details>Unaligned and non-gain corrected, 40-frame movies (K2 counting mode) were collected with EPU using a Titan Krios operating at 300 kV (LMB Krios I). The exposure was at  32.6 e/A^2) with a defocus range of -2.8 to -1.5 um. Micrographs were manually picked in relion using start-end helical picking. Gain reference is in Movies/Case2-gain-ref.MRC. Have fun twice.</details>
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        <pickedParticlesDirectory>data/EMPIAR_upload/ManualPick/Case2/job004</pickedParticlesDirectory>
    </imageSet>
    <imageSet>
        <name>Unaligned movies of alpha-synuclein filament seeded in vitro by filaments purified from Multiple Systems Atrophy Case 5</name>
        <directory>/data/EMPIAR_upload/Movies/Case5</directory>
        <category>micrographs - multiframe</category>
        <headerFormat>TIFF</headerFormat>
        <dataFormat>TIFF</dataFormat>
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            <imageHeight>3710</imageHeight>
            <pixelHeight>1.14</pixelHeight>
        </dimensions>
        <details>Unaligned and non-gain corrected, 40-frame movies (K2 counting mode) were collected with EPU using a Titan Krios operating at 300 kV (LMB Krios I). The exposure was at  37.5 e/A^2) with a defocus range of -2.8 to -1.5 um. Micrographs were manually picked in relion using start-end helical picking. Gain reference is in Movies/Case5-gain-ref.MRC. Have fun thrice.</details>
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        <pickedParticlesDirectory>data/EMPIAR_upload/ManualPick/Case5/job005</pickedParticlesDirectory>
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    <imageSet>
        <name>Type 1A particles after Bayesian polishing</name>
        <directory>/data/EMPIAR_upload/PolishedParticles/Type1A</directory>
        <category>picked particles - single frame - processed</category>
        <headerFormat>MRCS</headerFormat>
        <dataFormat>MRCS</dataFormat>
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        <voxelType>32 BIT FLOAT</voxelType>
        <dimensions>
            <imageWidth>256</imageWidth>
            <pixelWidth>1.14</pixelWidth>
            <imageHeight>256</imageHeight>
            <pixelHeight>1.14</pixelHeight>
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        <details>Polished particles for Type1A</details>
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        <micrographsFilePattern></micrographsFilePattern>
        <pickedParticlesFilePattern></pickedParticlesFilePattern>
        <pickedParticlesDirectory></pickedParticlesDirectory>
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    <imageSet>
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        <directory>/data/EMPIAR_upload/PolishedParticles/Type2A</directory>
        <category>picked particles - single frame - processed</category>
        <headerFormat>MRCS</headerFormat>
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        <framesPerImage>40</framesPerImage>
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            <pixelHeight>1.14</pixelHeight>
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        <details>Polished particles for Type 2A</details>
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        <directory>/data/EMPIAR_upload/PolishedParticles/Type1B</directory>
        <category>picked particles - single frame - processed</category>
        <headerFormat>MRCS</headerFormat>
        <dataFormat>MRCS</dataFormat>
        <numImagesOrTiltSeries>33479</numImagesOrTiltSeries>
        <framesPerImage>40</framesPerImage>
        <voxelType>32 BIT FLOAT</voxelType>
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            <pixelWidth>1.1</pixelWidth>
            <imageHeight>256</imageHeight>
            <pixelHeight>1.1</pixelHeight>
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        <details>Polished particles for Type 1B</details>
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        <pickedParticlesDirectory></pickedParticlesDirectory>
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    <imageSet>
        <name>Type 2B particles after Bayesian polishing</name>
        <directory>/data/EMPIAR_upload/PolishedParticles/Type2B</directory>
        <category>picked particles - single frame - processed</category>
        <headerFormat>MRCS</headerFormat>
        <dataFormat>MRCS</dataFormat>
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        <framesPerImage>40</framesPerImage>
        <voxelType>32 BIT FLOAT</voxelType>
        <dimensions>
            <imageWidth>256</imageWidth>
            <pixelWidth>1.1</pixelWidth>
            <imageHeight>256</imageHeight>
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        <details>Polished particles for Type 2B</details>
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        <directory>/data/EMPIAR_upload/PolishedParticles/Type2AB</directory>
        <category>picked particles - single frame - processed</category>
        <headerFormat>MRCS</headerFormat>
        <dataFormat>MRCS</dataFormat>
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        <framesPerImage>40</framesPerImage>
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            <imageHeight>256</imageHeight>
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        </dimensions>
        <details>Polished particles for Type 2AB</details>
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        <pickedParticlesFilePattern></pickedParticlesFilePattern>
        <pickedParticlesDirectory></pickedParticlesDirectory>
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        <directory>/data/EMPIAR_upload/PolishedParticles/Type3</directory>
        <category>picked particles - single frame - processed</category>
        <headerFormat>MRCS</headerFormat>
        <dataFormat>MRCS</dataFormat>
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        <framesPerImage>40</framesPerImage>
        <voxelType>32 BIT FLOAT</voxelType>
        <dimensions>
            <imageWidth>256</imageWidth>
            <pixelWidth>1.14</pixelWidth>
            <imageHeight>256</imageHeight>
            <pixelHeight>1.14</pixelHeight>
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        <details>Polished particles for Type 3</details>
        <segmentationList/>
        <micrographsFilePattern></micrographsFilePattern>
        <pickedParticlesFilePattern></pickedParticlesFilePattern>
        <pickedParticlesDirectory></pickedParticlesDirectory>
    </imageSet>
</entry>
