<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-10559" schemaVersion="0.65" public="true">
    <admin>
        <currentStatus>REL</currentStatus>
        <keyDates>
            <depositionDate>2020-11-17</depositionDate>
            <releaseDate>2020-11-24</releaseDate>
            <updateDate>2021-06-30</updateDate>
        </keyDates>
        <title>Krios G4 apoferritin test with K3/BioQuantum SerialEM BIS 3x3x1</title>
        <correspondingAuthor private="true">
            <authorORCID>0000-0001-6406-8993</authorORCID>
            <firstName>Radostin</firstName>
            <lastName>Danev</lastName>
            <organization type="academic">The University of Tokyo</organization>
            <street>7-3-1 Hongo, Bunkyo-ku</street>
            <townOrCity>Toyko</townOrCity>
            <country>Japan</country>
            <postOrZipCode>113-0033</postOrZipCode>
        </correspondingAuthor>
        <principalInvestigator private="true">
            <authorORCID>0000-0001-6406-8993</authorORCID>
            <firstName>Radostin</firstName>
            <lastName>Danev</lastName>
            <organization type="academic">The University of Tokyo</organization>
            <street>7-3-1 Hongo, Bunkyo-ku</street>
            <townOrCity>Toyko</townOrCity>
            <country>Japan</country>
            <postOrZipCode>113-0033</postOrZipCode>
        </principalInvestigator>
        <authorsList>
            <author authorORCID="0000-0001-6406-8993">Danev R</author>
        </authorsList>
        <datasetSize units="GB">659.0</datasetSize>
        <entryDOI>10.6019/EMPIAR-10559</entryDOI>
        <experimentType>EMDB</experimentType>
    </admin>
    <crossReferences>
        <relatedEMDBEntries>
            <emdbEntry>EMD-30683</emdbEntry>
        </relatedEMDBEntries>
        <citationList>
            <universalCitation>
                <journalCitation published="true" preprint="false">
                    <author authorORCID="0000-0001-6406-8993" order="1">Danev R</author>
                    <author order="2">Yanagisawa H</author>
                    <author order="3">Kikkawa M</author>
                    <title>Cryo-EM Performance Testing of Hardware and Data Acquisition Strategies</title>
                    <journal>Microscopy (Oxford, England)</journal>
                    <journalAbbreviation>Microscopy (Oxf)</journalAbbreviation>
                    <country></country>
                    <issue>1</issue>
                    <volume>1</volume>
                    <firstPage>1</firstPage>
                    <lastPage>2</lastPage>
                    <year>2021</year>
                    <language>English</language>
                    <externalReferences type="doi">10.1093/jmicro/dfab016</externalReferences>
                    <externalReferences type="pubmed">33969878</externalReferences>
                </journalCitation>
            </universalCitation>
        </citationList>
    </crossReferences>
    <imageSet>
        <name>Unaligned multi-frame non-gain-normalized movies in LZW compressed TIFF format</name>
        <directory>/data</directory>
        <category>micrographs - multiframe</category>
        <headerFormat>TIFF</headerFormat>
        <dataFormat>TIFF</dataFormat>
        <numImagesOrTiltSeries>2391</numImagesOrTiltSeries>
        <framesPerImage>76</framesPerImage>
        <voxelType>UNSIGNED BYTE</voxelType>
        <dimensions>
            <imageWidth>11520</imageWidth>
            <pixelWidth>0.1997</pixelWidth>
            <imageHeight>8184</imageHeight>
            <pixelHeight>0.1997</pixelHeight>
        </dimensions>
        <details>Please see the "dataset_details_apoF.txt" file for details.

To test the overall performance of the Krios G4 at The University of Tokyo, five datasets were collected from the same apoferritin grid in the beginning of July 2020.
This was the first dataset in the series.

Sample: mouse heavy chain apoferritin
Grid: UltrAuFoil 300 mesh R1.2/1.3
Cemera: Gatan K3 post a BioQuantum energy filter
Camera mode: super resolution, CDS
TEM mode: EFTEM NanoProbe
Mag: x215k
C2 aperture: 50 um
Spot: 4
Beam diameter: 1.55 um
EF slit: 15 eV
Data collection software: SerialEM
Acquisition method: beam-image shift with beam-tilt compensation
Acquisition pattern: 3 x 3 holes, 1 image in the center of each hole
Physical Pixel: 0.3994 A/pix
SuperRes pixel: 0.1997 A/pix
Exposure rate:  3.42 e/pix/s (CDS)
Exposure time:  3.04 s
Total exposure: 64.5 e/A2 
Frames: 76
Defocus: 0.2 - 0.8 um
Movies: 2391
Data format: non-gain-normalized LZW compressed TIFFs
Gain reference: "apoF_gain.mrc" prepared from the data
Final particles: 181k
Particles file: "run_data.star"
Optics groups: per-acquisition position and per hour
Resolution (with Ewald correction): 1.31 A
Rosenthal-Henderson B-factor: 38.7 A^2


Rado
November 19, 2020</details>
        <segmentationList/>
        <micrographsFilePattern>data/*.tif</micrographsFilePattern>
        <pickedParticlesFilePattern>data/run_data.star</pickedParticlesFilePattern>
        <pickedParticlesDirectory></pickedParticlesDirectory>
    </imageSet>
</entry>
