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    <admin>
        <lastUpdate>2013-10-02</lastUpdate>
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    <deposition>
        <status prior="REL">OBS</status>
        <depositionDate>2013-05-28</depositionDate>
        <depositionSite>PDBe</depositionSite>
        <processingSite>PDBe</processingSite>
        <headerReleaseDate>2013-07-03</headerReleaseDate>
        <mapReleaseDate>2013-10-02</mapReleaseDate>
        <obsoletedDate>2013-10-02</obsoletedDate>
        <details>Author requested withdrawal of this entry</details>
        <title>Tomographic reconstruction of unstained, frozen-hydrated thylakoid membranes from spinach chloroplasts.</title>
        <authors>Ford RC, Holzenburg A</authors>
        <keywords>Photosynthesis, thylakoid membrane, CF1-CF0 proton ATPase, photosystem, cytochrome b6f, ribosome, chloroplast.</keywords>
        <primaryReference published="true">
            <journalArticle>
                <authors>Ford RC, Holzenburg A</authors>
                <articleTitle>Organization of protein complexes and a mechanism for grana formation in photosynthetic membranes as revealed by cryo-electron microscopy</articleTitle>
                <journal>Crystal Research and Technology</journal>
                <volume>n/a</volume>
                <firstPage>n/a</firstPage>
                <lastPage>n/a</lastPage>
                <year>2013</year>
                <externalReference type="doi">doi:10.1002/crat.201300116</externalReference>
            </journalArticle>
        </primaryReference>
    </deposition>
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        <dataType>Image stored as Integer*2</dataType>
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            <cellAlpha units="degrees">90.0</cellAlpha>
            <cellBeta units="degrees">90.0</cellBeta>
            <cellGamma units="degrees">90.0</cellGamma>
        </cell>
        <axisOrder>
            <axisOrderFast>X</axisOrderFast>
            <axisOrderMedium>Y</axisOrderMedium>
            <axisOrderSlow>Z</axisOrderSlow>
        </axisOrder>
        <statistics>
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            <maximum>243.00000000</maximum>
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        <details>::::EMDATABANK.org::::EMD-2388::::</details>
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            <pixelX units="A">8.8</pixelX>
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            <pixelZ units="A">8.8</pixelZ>
        </pixelSpacing>
        <contourLevel source="author">118</contourLevel>
        <annotationDetails>Tomogram of thylakoid membranes</annotationDetails>
    </map>
    <supplement>
        <maskSet/>
        <sliceSet/>
        <figureSet>
            <figure>
                <file>emd_2388.tif</file>
            </figure>
        </figureSet>
        <fscSet/>
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    <sample>
        <numComponents>1</numComponents>
        <name>Thylakoid membrane from spinach.</name>
        <sampleComponentList>
            <sampleComponent componentID="1">
                <entry>cellular-component</entry>
                <sciName>Thylakoid membrane</sciName>
                <synName>Photosynthetic membrane</synName>
                <details>Buffer - 20mM MES, 5mM MgCl2, 15mM NaCl, pH6.5, 150mM sorbitol. 3microlitres of membranes at 2mg per ml chlorophyll were directly applied to electron microscope grids (Quantifoil carbon grids with 1.2 micron holes). After blotting excess liquid, (2x 1s blots at 95 percent relative humidity in a Vitrobot device), the grids were rapidly frozen by plunging into liquid ethane and transferred at less than 110K to the Gatan cryo-stage of the electron microscope.</details>
                <cellular-component>
                    <recombinantExpFlag>false</recombinantExpFlag>
                    <sciSpeciesName ncbiTaxId="3562">Spinacia oleracea</sciSpeciesName>
                    <synSpeciesName>Spinach</synSpeciesName>
                    <externalReferences/>
                    <natSource>
                        <organOrTissue>Leaf</organOrTissue>
                        <organelle>Chloroplast</organelle>
                    </natSource>
                    <engSource/>
                </cellular-component>
            </sampleComponent>
        </sampleComponentList>
    </sample>
    <experiment>
        <vitrification>
            <method>2 x 1 sec blots before plunging.</method>
            <cryogenName>NITROGEN</cryogenName>
            <details>Vitrification instrument: Vitrobot FEI. Rapid plunging into liquid ethane.</details>
            <humidity>95</humidity>
            <instrument>FEI VITROBOT MARK I</instrument>
            <temperature units="Kelvin">97</temperature>
        </vitrification>
        <imaging>
            <astigmatism>Astigmatism corrected by live FFT.</astigmatism>
            <electronSource>FIELD EMISSION GUN</electronSource>
            <electronDose units="e/A**2">45</electronDose>
            <imagingMode>BRIGHT FIELD</imagingMode>
            <nominalDefocusMin units="nm">8000</nominalDefocusMin>
            <temperatureMin units="Kelvin">96</temperatureMin>
            <nominalDefocusMax units="nm">8000</nominalDefocusMax>
            <illuminationMode>FLOOD BEAM</illuminationMode>
            <temperatureMax units="Kelvin">98</temperatureMax>
            <specimenHolder>Single tilt</specimenHolder>
            <nominalCs units="mm">2.0</nominalCs>
            <tiltAngleMin units="degrees">-65</tiltAngleMin>
            <calibratedMagnification>33998</calibratedMagnification>
            <tiltAngleMax units="degrees">49</tiltAngleMax>
            <temperature units="Kelvin">97</temperature>
            <microscope>FEI TECNAI F20</microscope>
            <date>28-JUL-2009</date>
            <specimenHolderModel>GATAN LIQUID NITROGEN</specimenHolderModel>
            <acceleratingVoltage units="kV">200</acceleratingVoltage>
            <nominalMagnification>34000</nominalMagnification>
        </imaging>
        <imageAcquisition>
            <numDigitalImages>77</numDigitalImages>
            <samplingSize units="microns">15</samplingSize>
        </imageAcquisition>
        <fitting/>
        <specimenPreparation>
            <staining>No stain.</staining>
            <specimenState>tissue</specimenState>
            <specimenConc units="mg/ml">2</specimenConc>
            <specimenSupportDetails>Quantifoil 400mesh carbon grids with 1.2 micron holes.</specimenSupportDetails>
            <buffer>
                <details>20mM MES, 5mM MgCl2, 15mM NaCl, pH6.5, 150mM sorbitol.</details>
                <ph>6.5</ph>
            </buffer>
        </specimenPreparation>
    </experiment>
    <processing>
        <method>tomography</method>
        <reconstruction>
            <software>eTOMO</software>
            <details>Standard eTOMO procedures for single axis tilt tomograms. Fiducials were selected from the tomogram and tracked in each image by hand initially.</details>
            <resolutionByAuthor>45</resolutionByAuthor>
            <resolutionMethod>Resolution of known features of complexes</resolutionMethod>
        </reconstruction>
        <tomography>
            <appliedSymmetry>C1</appliedSymmetry>
            <tiltAngleIncrement>1</tiltAngleIncrement>
            <numSections>57</numSections>
            <details>1 degree increments above 45 deg, 2.5 degree increments below this.</details>
        </tomography>
    </processing>
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