<?xml version="1.0" encoding="UTF-8"?>
<emdEntry accessCode="3000" version="1.9.6">
    <admin>
        <lastUpdate>2016-05-11</lastUpdate>
    </admin>
    <deposition>
        <status prior="HPUB">OBS</status>
        <depositionDate>2015-05-07</depositionDate>
        <depositionSite>PDBe</depositionSite>
        <processingSite>PDBe</processingSite>
        <headerReleaseDate>2015-06-17</headerReleaseDate>
        <obsoletedDate>2015-12-16</obsoletedDate>
        <supersededByList>
            <entry>EMD-3283</entry>
        </supersededByList>
        <details>Data was reprocessed</details>
        <title>The Structure of Human BK Polyomavirus at 6.5 A resolution</title>
        <authors>Hurdiss D, Thompson R, Prescott EL, Panou M, Macdonald A, Ranson NA</authors>
        <keywords>BK Polyomavirus, BKPyV, BKV</keywords>
        <primaryReference published="false">
            <journalArticle>
                <authors>Hurdiss D, Thompson R, Prescott EL, Panou M, Macdonald A, Ranson NA</authors>
                <articleTitle>The Structure of Human BK Polyomavirus at 6.5 A resolution</articleTitle>
                <journal>To Be Published</journal>
                <volume/>
                <firstPage/>
                <lastPage/>
                <year/>
            </journalArticle>
        </primaryReference>
    </deposition>
    <map>
        <file format="CCP4" sizeKb="221185" type="map">emd_3000.map.gz</file>
        <dataType>Image stored as Reals</dataType>
        <dimensions>
            <numColumns>384</numColumns>
            <numRows>384</numRows>
            <numSections>384</numSections>
        </dimensions>
        <origin>
            <originCol>-192</originCol>
            <originRow>-192</originRow>
            <originSec>-192</originSec>
        </origin>
        <limit>
            <limitCol>191</limitCol>
            <limitRow>191</limitRow>
            <limitSec>191</limitSec>
        </limit>
        <spacing>
            <spacingCol>384</spacingCol>
            <spacingRow>384</spacingRow>
            <spacingSec>384</spacingSec>
        </spacing>
        <cell>
            <cellA units="A">691.19995</cellA>
            <cellB units="A">691.19995</cellB>
            <cellC units="A">691.19995</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>-0.02679493</minimum>
            <maximum>0.07481748</maximum>
            <average>0.00121312</average>
            <std>0.00959812</std>
        </statistics>
        <spaceGroupNumber>1</spaceGroupNumber>
        <details>::::EMDATABANK.org::::EMD-3000::::</details>
        <pixelSpacing>
            <pixelX units="A">1.7999998</pixelX>
            <pixelY units="A">1.7999998</pixelY>
            <pixelZ units="A">1.7999998</pixelZ>
        </pixelSpacing>
        <contourLevel source="author">0.025</contourLevel>
        <annotationDetails>Reconstruction of BK polyomavirus (sharpened map)</annotationDetails>
    </map>
    <supplement>
        <maskSet/>
        <sliceSet/>
        <figureSet/>
        <fscSet>
            <fsc>
                <file>emd_3000_fsc.xml</file>
            </fsc>
        </fscSet>
    </supplement>
    <sample>
        <numComponents>1</numComponents>
        <name>BK Polyomavirus</name>
        <compDegree>Icosohedral</compDegree>
        <sampleComponentList>
            <sampleComponent componentID="1">
                <entry>virus</entry>
                <sciName>BK polyomavirus</sciName>
                <virus>
                    <sciSpeciesName ncbiTaxId="10629">BK polyomavirus</sciSpeciesName>
                    <sciSpeciesStrain>Dunlop</sciSpeciesStrain>
                    <empty>false</empty>
                    <enveloped>false</enveloped>
                    <isolate>STRAIN</isolate>
                    <class>VIRION</class>
                    <externalReferences/>
                    <natSource>
                        <hostSpecies ncbiTaxId="9606">Homo sapiens</hostSpecies>
                        <hostCategory>VERTEBRATES</hostCategory>
                    </natSource>
                    <engSource>
                        <expSystemCell>Vero</expSystemCell>
                        <expSystem ncbiTaxId="9534">Chlorocebus aethiops</expSystem>
                    </engSource>
                </virus>
            </sampleComponent>
        </sampleComponentList>
    </sample>
    <experiment>
        <vitrification>
            <method>6.5 seconds blot before plunging</method>
            <cryogenName>ETHANE</cryogenName>
            <humidity>100</humidity>
            <instrument>FEI VITROBOT MARK IV</instrument>
        </vitrification>
        <imaging>
            <electronSource>FIELD EMISSION GUN</electronSource>
            <electronDose units="e/A**2">40</electronDose>
            <imagingMode>BRIGHT FIELD</imagingMode>
            <nominalDefocusMin units="nm">600</nominalDefocusMin>
            <nominalDefocusMax units="nm">4800</nominalDefocusMax>
            <illuminationMode>FLOOD BEAM</illuminationMode>
            <specimenHolder>626b</specimenHolder>
            <detector>GATAN K2 (4k x 4k)</detector>
            <nominalCs units="mm">2</nominalCs>
            <tiltAngleMin units="degrees">0</tiltAngleMin>
            <tiltAngleMax units="degrees">0</tiltAngleMax>
            <microscope>FEI TECNAI F20</microscope>
            <date>12-DEC-2014</date>
            <specimenHolderModel>GATAN LIQUID NITROGEN</specimenHolderModel>
            <acceleratingVoltage units="kV">200</acceleratingVoltage>
            <nominalMagnification>19000</nominalMagnification>
        </imaging>
        <imageAcquisition>
            <numDigitalImages>432</numDigitalImages>
        </imageAcquisition>
        <fitting/>
        <specimenPreparation>
            <specimenState>particle</specimenState>
            <specimenSupportDetails>Quantifoil R2/1 EM grids</specimenSupportDetails>
            <buffer>
                <details>10mM HEPES pH 7.9, 1mM CaCl2, 1mM MgCl2, 5mM KCl</details>
                <ph>7.4</ph>
            </buffer>
        </specimenPreparation>
    </experiment>
    <processing>
        <method>singleParticle</method>
        <reconstruction>
            <software>Relion</software>
            <ctfCorrection>CTFFIND3</ctfCorrection>
            <resolutionByAuthor>6.55</resolutionByAuthor>
            <resolutionMethod>FSC 0.143, gold-standard</resolutionMethod>
        </reconstruction>
        <singleParticle>
            <appliedSymmetry>I</appliedSymmetry>
            <numProjections>3394</numProjections>
        </singleParticle>
    </processing>
</emdEntry>
