<?xml version="1.0" encoding="UTF-8"?>
<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="https://github.com/emdb-empiar/emdb-schemas/blob/master/v3/v3_0_1_4/emdb.xsd" emdb_id="EMD-0378" version="3.0.1.4">
    <admin>
        <current_status>
            <date>2019-06-05</date>
            <code>REL</code>
            <processing_site>RCSB</processing_site>
        </current_status>
        <sites>
            <deposition>RCSB</deposition>
            <last_processing>RCSB</last_processing>
        </sites>
        <key_dates>
            <deposition>2018-12-03</deposition>
            <header_release>2018-12-12</header_release>
            <map_release>2019-04-24</map_release>
            <update>2019-06-05</update>
        </key_dates>
        <title>p53 dimer assembly</title>
        <authors_list>
            <author>Kelly DF</author>
            <author>Dearnaley WJ</author>
            <author>Varano AC</author>
        </authors_list>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Alden NA</author>
                    <author order="2">Varano AC</author>
                    <author order="3">Dearnaley WJ</author>
                    <author order="4">Solares MJ</author>
                    <author order="5">Luqiu WY</author>
                    <author order="6">Liang Y</author>
                    <author order="7">Sheng Z</author>
                    <author order="8">McDonald SM</author>
                    <author order="9">Damiano J</author>
                    <author order="10">McConnell J</author>
                    <author order="11">Dukes MJ</author>
                    <author order="12">Kelly DF</author>
                    <title>Cryo-EM-On-a-Chip: Custom-Designed Substrates for the 3D Analysis of Macromolecules.</title>
                    <journal_abbreviation>Small</journal_abbreviation>
                    <country>DE</country>
                    <volume>15</volume>
                    <first_page>e1900918</first_page>
                    <last_page>e1900918</last_page>
                    <year>2019</year>
                    <external_references type="PUBMED">30963664</external_references>
                    <external_references type="DOI">doi:10.1002/smll.201900918</external_references>
                    <external_references type="ISSN">1613-6829</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-0378</emdb_id>
                <relationship>
                    <other>associated EM volume</other>
                </relationship>
            </emdb_reference>
        </emdb_list>
    </crossreferences>
    <sample>
        <name>p53 dimer assembly</name>
        <supramolecule_list>
            <complex_supramolecule supramolecule_id="1">
                <name>p53 dimer assembly</name>
                <parent>0</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>1</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                    <organ>Brain</organ>
                    <tissue>Glioblastoma</tissue>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.116</theoretical>
                </molecular_weight>
            </complex_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>p53</name>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Human</organism>
                    <organ>Brain</organ>
                    <tissue>Glioblastoma</tissue>
                </natural_source>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGP
DEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAK
SVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHE
RCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNS
SCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGEPHHELP
PGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPG
GSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD</string>
                </sequence>
            </protein_or_peptide>
        </macromolecule_list>
    </sample>
    <structure_determination_list>
        <structure_determination structure_determination_id="1">
            <method>singleParticle</method>
            <aggregation_state>particle</aggregation_state>
            <specimen_preparation_list>
                <single_particle_preparation preparation_id="1">
                    <concentration units="mg/mL">0.02</concentration>
                    <buffer>
                        <ph>7.2</ph>
                        <component>
                            <name>HEPES buffer</name>
                        </component>
                        <details>20 mM HEPES, pH 7.2, 150 mM NaCl, 10 mM CaCl2, 10 mM MgCl2, 60 mM Imidazole</details>
                    </buffer>
                    <grid>
                        <material>SILICON NITRIDE</material>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">90</chamber_humidity>
                        <chamber_temperature units="K">298</chamber_temperature>
                        <instrument>FEI VITROBOT MARK III</instrument>
                        <details>Blot for 6-10 seconds before plunging, dwell time was 1 second, grid platform was SiN chip.. </details>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>FEI TECNAI SPIRIT</microscope>
                    <illumination_mode>FLOOD BEAM</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>LAB6</electron_source>
                    <acceleration_voltage units="kV">120</acceleration_voltage>
                    <nominal_cs units="mm">2.0</nominal_cs>
                    <nominal_defocus_min units="µm">-1.5</nominal_defocus_min>
                    <nominal_magnification>68000.</nominal_magnification>
                    <specimen_holder_model>SIDE ENTRY, EUCENTRIC</specimen_holder_model>
                    <cooling_holder_cryogen>NITROGEN</cooling_holder_cryogen>
                    <alignment_procedure>
                        <basic/>
                    </alignment_procedure>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>FEI EAGLE (2k x 2k)</film_or_detector_model>
                            <digitization_details>
                                <sampling_interval units="µm">30.0</sampling_interval>
                            </digitization_details>
                            <number_grids_imaged>1</number_grids_imaged>
                            <number_real_images>100</number_real_images>
                            <average_electron_dose_per_image units="e/Å^2">5.0</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <image_recording_id>1</image_recording_id>
                <particle_selection>
                    <number_selected>12144</number_selected>
                </particle_selection>
                <ctf_correction>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>2.1</version>
                        </software>
                    </software_list>
                </ctf_correction>
                <startup_model type_of_model="PDB ENTRY">
                    <pdb_model>
                        <pdb_id>2AC0</pdb_id>
                    </pdb_model>
                    <details>Resolution filtered to ~50 Angstrom</details>
                </startup_model>
                <final_reconstruction>
                    <applied_symmetry>
                        <point_group>C2</point_group>
                    </applied_symmetry>
                    <resolution units="Å" res_type="BY AUTHOR">10.0</resolution>
                    <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>2.1</version>
                        </software>
                    </software_list>
                    <number_images_used>12144</number_images_used>
                </final_reconstruction>
                <initial_angle_assignment>
                    <type>OTHER</type>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>2.1</version>
                        </software>
                    </software_list>
                    <details>Empirical Bayesian approach</details>
                </initial_angle_assignment>
                <final_angle_assignment>
                    <type>OTHER</type>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>2.1</version>
                        </software>
                    </software_list>
                    <details>Empirical Bayesian approach</details>
                </final_angle_assignment>
                <final_three_d_classification>
                    <number_classes>1</number_classes>
                    <average_number_members_per_class>12144.0</average_number_members_per_class>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>2.1</version>
                        </software>
                    </software_list>
                </final_three_d_classification>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="4001">
        <file>emd_0378.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>100</col>
            <row>100</row>
            <sec>100</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>100</x>
            <y>100</y>
            <z>100</z>
        </spacing>
        <cell>
            <a units="Å">419.99997</a>
            <b units="Å">419.99997</b>
            <c units="Å">419.99997</c>
            <alpha units="deg">90.0</alpha>
            <beta units="deg">90.0</beta>
            <gamma units="deg">90.0</gamma>
        </cell>
        <axis_order>
            <fast>X</fast>
            <medium>Y</medium>
            <slow>Z</slow>
        </axis_order>
        <statistics>
            <minimum>-0.55717945</minimum>
            <maximum>1.3238852</maximum>
            <average>0.0038478214</average>
            <std>0.03233218</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">4.2</x>
            <y units="Å">4.2</y>
            <z units="Å">4.2</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.569</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-0378::::</label>
        <annotation_details>p53 dimer assembly</annotation_details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <initial_model>
                    <access_code>2AC0</access_code>
                </initial_model>
                <refinement_protocol>RIGID BODY FIT</refinement_protocol>
                <refinement_space>REAL</refinement_space>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>
