<?xml version="1.0" encoding="UTF-8"?>
<emdEntry accessCode="3060" version="1.9.6">
    <admin>
        <lastUpdate>2016-02-10</lastUpdate>
    </admin>
    <deposition>
        <status prior="HPUB">OBS</status>
        <depositionDate>2015-06-22</depositionDate>
        <depositionSite>PDBe</depositionSite>
        <processingSite>PDBe</processingSite>
        <headerReleaseDate>2015-08-12</headerReleaseDate>
        <obsoletedDate>2016-02-10</obsoletedDate>
        <supersededByList>
            <entry>EMD-3233</entry>
        </supersededByList>
        <details>Data was reprocessed.</details>
        <title>Phase plate structure of Peroxiredoxin-3 dodecamers</title>
        <authors>Khoshouei M, Radjainia M, Abrishami V, Phillips AJ, Gerrard JA, Mitra AK, Plitzko JM, Baumeister W, Danev R</authors>
        <keywords>Volta phase plate, peroxiredoxin, peroxidase, antioxidant</keywords>
        <primaryReference published="false">
            <journalArticle>
                <authors>Khoshouei M, Radjainia M, Abrishami V, Phillips AJ, Gerrard JA, Mitra AK, Plitzko JM, Baumeister W, Danev R</authors>
                <articleTitle>Volta phase plate cryo-EM of the small protein complex Prx3</articleTitle>
                <journal>NAT.COMMUN.</journal>
                <volume/>
                <firstPage/>
                <lastPage/>
                <year/>
            </journalArticle>
        </primaryReference>
    </deposition>
    <map>
        <file format="CCP4" sizeKb="13719" type="map">emd_3060.map.gz</file>
        <dataType>Image stored as Reals</dataType>
        <dimensions>
            <numColumns>152</numColumns>
            <numRows>152</numRows>
            <numSections>152</numSections>
        </dimensions>
        <origin>
            <originCol>0</originCol>
            <originRow>0</originRow>
            <originSec>0</originSec>
        </origin>
        <limit>
            <limitCol>151</limitCol>
            <limitRow>151</limitRow>
            <limitSec>151</limitSec>
        </limit>
        <spacing>
            <spacingCol>152</spacingCol>
            <spacingRow>152</spacingRow>
            <spacingSec>152</spacingSec>
        </spacing>
        <cell>
            <cellA units="A">205.2</cellA>
            <cellB units="A">205.2</cellB>
            <cellC units="A">205.2</cellC>
            <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>
            <minimum>-0.07650846</minimum>
            <maximum>0.11458807</maximum>
            <average>0.00075023</average>
            <std>0.00704310</std>
        </statistics>
        <spaceGroupNumber>1</spaceGroupNumber>
        <details>::::EMDATABANK.org::::EMD-3060::::</details>
        <pixelSpacing>
            <pixelX units="A">1.35</pixelX>
            <pixelY units="A">1.35</pixelY>
            <pixelZ units="A">1.35</pixelZ>
        </pixelSpacing>
        <contourLevel source="author">0.024</contourLevel>
        <annotationDetails>Single-particle reconstruction of Prx3 dodecamers from Volta Phase Contrast Images</annotationDetails>
    </map>
    <supplement>
        <maskSet/>
        <sliceSet/>
        <figureSet/>
        <fscSet>
            <fsc>
                <file>emd_3060_fsc.xml</file>
            </fsc>
        </fscSet>
    </supplement>
    <sample>
        <numComponents>1</numComponents>
        <name>Peroxiredoxin-3 dodecamers</name>
        <compDegree>12</compDegree>
        <molWtTheo units="MDa">0.257</molWtTheo>
        <details>The sample was monodisperse</details>
        <molWtMethod>SEC and MS</molWtMethod>
        <molWtExp units="MDa">0.257</molWtExp>
        <sampleComponentList>
            <sampleComponent componentID="1">
                <entry>protein</entry>
                <sciName>Human Peroxiredoxin-3</sciName>
                <synName>Prx3</synName>
                <molWtTheo units="MDa">0.257</molWtTheo>
                <molWtExp units="MDa">0.257</molWtExp>
                <protein>
                    <sciSpeciesName ncbiTaxId="9606">Homo sapiens</sciSpeciesName>
                    <recombinantExpFlag>true</recombinantExpFlag>
                    <oligomericDetails>dodecamer</oligomericDetails>
                    <synSpeciesName>Human</synSpeciesName>
                    <numCopies>1</numCopies>
                    <externalReferences>
                        <refUniProt>P30048</refUniProt>
                    </externalReferences>
                    <natSource>
                        <organelle>Mitochondria</organelle>
                        <cellLocation>matrix</cellLocation>
                    </natSource>
                    <engSource>
                        <expSystem ncbiTaxId="562">Escherichia coli</expSystem>
                    </engSource>
                </protein>
            </sampleComponent>
        </sampleComponentList>
    </sample>
    <experiment>
        <vitrification>
            <cryogenName>ETHANE</cryogenName>
            <instrument>FEI VITROBOT MARK III</instrument>
        </vitrification>
        <imaging>
            <electronSource>FIELD EMISSION GUN</electronSource>
            <imagingMode>BRIGHT FIELD</imagingMode>
            <illuminationMode>FLOOD BEAM</illuminationMode>
            <detector>GATAN K2 (4k x 4k)</detector>
            <microscope>FEI TITAN KRIOS</microscope>
            <date>26-FEB-2015</date>
            <specimenHolderModel>FEI TITAN KRIOS AUTOGRID HOLDER</specimenHolderModel>
            <acceleratingVoltage units="kV">300</acceleratingVoltage>
        </imaging>
        <imageAcquisition>
            <numDigitalImages>44</numDigitalImages>
        </imageAcquisition>
        <fitting/>
        <specimenPreparation>
            <specimenState>particle</specimenState>
            <specimenConc units="mg/ml">1</specimenConc>
            <specimenSupportDetails>Quantifoil R2/2</specimenSupportDetails>
            <buffer>
                <details>20mM Hepes pH8, 150m NaCl</details>
                <ph>8</ph>
            </buffer>
        </specimenPreparation>
    </experiment>
    <processing>
        <method>singleParticle</method>
        <reconstruction>
            <software>Relion</software>
            <resolutionByAuthor>7.3</resolutionByAuthor>
            <resolutionMethod>FSC 0.143, gold-standard</resolutionMethod>
        </reconstruction>
        <singleParticle>
            <appliedSymmetry>D6</appliedSymmetry>
            <numProjections>7000</numProjections>
        </singleParticle>
    </processing>
</emdEntry>
