<?xml version="1.0" encoding="UTF-8"?>
<emdEntry accessCode="6502" version="1.9.6">
    <admin>
        <lastUpdate>2016-03-09</lastUpdate>
    </admin>
    <deposition>
        <status prior="HPUB">OBS</status>
        <depositionDate>2015-11-03</depositionDate>
        <depositionSite>RCSB</depositionSite>
        <processingSite>PDBj</processingSite>
        <headerReleaseDate>2015-12-09</headerReleaseDate>
        <obsoletedDate>2016-03-09</obsoletedDate>
        <details>Obsoleted as per author's request</details>
        <title>Electron microscopy structure of monomeric ATM kinase</title>
        <authors>Lau WCY, Li Y, Liu Z, Gao Y, Zhang Q, Huen MSY</authors>
        <keywords>DNA damage, ATM kinase, Electron microscopy</keywords>
        <fittedPDBEntryIdList>
            <fittedPDBEntryId>3jc0</fittedPDBEntryId>
        </fittedPDBEntryIdList>
        <primaryReference published="false">
            <journalArticle>
                <authors>Lau WCY, Li Y, Liu Z, Gao Y, Zhang Q, Huen MSY</authors>
                <articleTitle>Structural insights into the regulatory mechanism of ATM kinase activation</articleTitle>
                <journal>To Be Published</journal>
                <volume/>
                <firstPage/>
                <lastPage/>
                <year/>
            </journalArticle>
        </primaryReference>
    </deposition>
    <map>
        <file format="CCP4" sizeKb="3908" type="map">emd_6502.map.gz</file>
        <dataType>Image stored as Reals</dataType>
        <dimensions>
            <numColumns>100</numColumns>
            <numRows>100</numRows>
            <numSections>100</numSections>
        </dimensions>
        <origin>
            <originCol>-50</originCol>
            <originRow>-50</originRow>
            <originSec>-50</originSec>
        </origin>
        <limit>
            <limitCol>49</limitCol>
            <limitRow>49</limitRow>
            <limitSec>49</limitSec>
        </limit>
        <spacing>
            <spacingCol>100</spacingCol>
            <spacingRow>100</spacingRow>
            <spacingSec>100</spacingSec>
        </spacing>
        <cell>
            <cellA units="A">461.0</cellA>
            <cellB units="A">461.0</cellB>
            <cellC units="A">461.0</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>-0.08145520</minimum>
            <maximum>1.07092738</maximum>
            <average>0.00547454</average>
            <std>0.05157611</std>
        </statistics>
        <spaceGroupNumber>1</spaceGroupNumber>
        <details>::::EMDATABANK.org::::EMD-6502::::</details>
        <pixelSpacing>
            <pixelX units="A">4.61</pixelX>
            <pixelY units="A">4.61</pixelY>
            <pixelZ units="A">4.61</pixelZ>
        </pixelSpacing>
        <contourLevel source="author">0.45</contourLevel>
        <annotationDetails>Reconstruction of monomeric ATM kinase</annotationDetails>
    </map>
    <supplement>
        <maskSet/>
        <sliceSet/>
        <figureSet/>
        <fscSet/>
    </supplement>
    <sample>
        <numComponents>1</numComponents>
        <name>Monomeric ATM kinase</name>
        <compDegree>1</compDegree>
        <molWtTheo units="MDa">0.35</molWtTheo>
        <details>The sample was monodisperse</details>
        <sampleComponentList>
            <sampleComponent componentID="1">
                <entry>protein</entry>
                <sciName>Monomeric ATM kinase</sciName>
                <molWtTheo units="MDa">0.35</molWtTheo>
                <protein>
                    <sciSpeciesName ncbiTaxId="9606">Homo sapiens</sciSpeciesName>
                    <recombinantExpFlag>true</recombinantExpFlag>
                    <oligomericDetails>Monomer</oligomericDetails>
                    <synSpeciesName>Human</synSpeciesName>
                    <numCopies>1</numCopies>
                    <externalReferences/>
                    <natSource/>
                    <engSource>
                        <vector>pcDNA-FLAG-His-ATM wt</vector>
                        <expSystem ncbiTaxId="9606">Homo sapiens</expSystem>
                        <expSystemCell>293T</expSystemCell>
                    </engSource>
                </protein>
            </sampleComponent>
        </sampleComponentList>
    </sample>
    <experiment>
        <vitrification>
            <cryogenName>NONE</cryogenName>
            <instrument>NONE</instrument>
        </vitrification>
        <imaging>
            <electronSource>LAB6</electronSource>
            <electronDose units="e/A**2">25</electronDose>
            <imagingMode>BRIGHT FIELD</imagingMode>
            <nominalDefocusMin units="nm">1000</nominalDefocusMin>
            <nominalDefocusMax units="nm">4000</nominalDefocusMax>
            <illuminationMode>FLOOD BEAM</illuminationMode>
            <detector>GATAN ULTRASCAN 4000 (4k x 4k)</detector>
            <nominalCs units="mm">2.0</nominalCs>
            <temperature units="Kelvin">296</temperature>
            <microscope>JEOL 2010</microscope>
            <date>01-JUL-2015</date>
            <specimenHolderModel>GATAN LIQUID NITROGEN</specimenHolderModel>
            <acceleratingVoltage units="kV">200</acceleratingVoltage>
            <nominalMagnification>50000</nominalMagnification>
        </imaging>
        <imageAcquisition>
            <numDigitalImages>251</numDigitalImages>
        </imageAcquisition>
        <fitting>
            <targetCriteria>cross correlation coefficient</targetCriteria>
            <details>Residues 2021-2118 are removed</details>
            <software>Chimera</software>
            <refProtocol>rigid body</refProtocol>
            <refSpace>REAL</refSpace>
            <pdbEntryIdList>
                <pdbEntryId>4JSV</pdbEntryId>
                <pdbChainId>A</pdbChainId>
            </pdbEntryIdList>
        </fitting>
        <specimenPreparation>
            <staining>2% w/v uranyl acetate</staining>
            <specimenState>particle</specimenState>
            <specimenConc units="mg/ml">0.02</specimenConc>
            <specimenSupportDetails>continuous carbon coated copper grids</specimenSupportDetails>
            <buffer>
                <details>25 mM Tris, 100 mM NaCl, 1 mM TCEP, 10% glycerol</details>
                <ph>8.0</ph>
            </buffer>
        </specimenPreparation>
    </experiment>
    <processing>
        <method>singleParticle</method>
        <reconstruction>
            <algorithm>projection matching</algorithm>
            <software>PRIME, EMAN2</software>
            <ctfCorrection>class average</ctfCorrection>
            <resolutionByAuthor>28</resolutionByAuthor>
            <resolutionMethod>FSC 0.143, gold-standard</resolutionMethod>
        </reconstruction>
        <singleParticle>
            <appliedSymmetry>C1</appliedSymmetry>
            <numProjections>6546</numProjections>
        </singleParticle>
    </processing>
</emdEntry>
