<?xml version="1.0" encoding="UTF-8"?>
<emd emdb_id="EMD-16220">
    <admin>
        <current_status>
            <date>2023-06-07</date>
            <code>REL</code>
            <processing_site>PDBe</processing_site>
        </current_status>
        <sites>
            <deposition>PDBe</deposition>
            <last_processing>PDBe</last_processing>
        </sites>
        <key_dates>
            <deposition>2022-11-23</deposition>
            <header_release>2023-05-31</header_release>
            <map_release>2023-05-31</map_release>
            <update>2023-06-07</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>European Research Council (ERC)</funding_body>
                <code>101018465</code>
                <country>European Union</country>
            </grant_reference>
            <grant_reference>
                <funding_body>German Research Foundation (DFG)</funding_body>
                <country>Germany</country>
            </grant_reference>
            <grant_reference>
                <funding_body>Netherlands Organisation for Scientific Research (NWO)</funding_body>
                <code>019.182EN.037</code>
                <country>Netherlands</country>
            </grant_reference>
            <grant_reference>
                <funding_body>European Union (EU)</funding_body>
                <code>899619</code>
                <country>European Union</country>
            </grant_reference>
        </grant_support>
        <title>Triple-stranded DNA as a structural element in DNA origami reinforced rod object</title>
        <authors_list>
            <author ORCID="0000-0002-2230-4553">Sachenbacher K</author>
            <author>Khoshouei A</author>
            <author ORCID="0000-0001-7805-906X">Honemann MN</author>
            <author ORCID="0000-0001-8779-9887">Engelen W</author>
            <author>Feigl E</author>
            <author ORCID="0000-0003-1270-3662">Dietz H</author>
        </authors_list>
        <keywords>DNA Origami, Triplex forming Oligo, Triplex, TFO, reinforced rod, rod, DNA</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Sachenbacher K</author>
                    <author order="2">Khoshouei A</author>
                    <author order="3">Honemann MN</author>
                    <author ORCID="0000-0001-8779-9887" order="4">Engelen W</author>
                    <author order="5">Feigl E</author>
                    <author ORCID="0000-0003-1270-3662" order="6">Dietz H</author>
                    <title>Triple-Stranded DNA As a Structural Element in DNA Origami.</title>
                    <journal_abbreviation>Acs Nano</journal_abbreviation>
                    <country>US</country>
                    <volume>17</volume>
                    <first_page>9014</first_page>
                    <last_page>9024</last_page>
                    <year>2023</year>
                    <external_references type="PUBMED">37159224</external_references>
                    <external_references type="DOI">doi:10.1021/acsnano.2c11402</external_references>
                    <external_references type="ISSN">1936-086X</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-16213</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
                <details>DNA origami object</details>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-16218</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
                <details>DNA origami object</details>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-16219</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
                <details>DNA origami object</details>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-16221</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
                <details>DNA origami object</details>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-16220</emdb_id>
                <relationship>
                    <other>associated EM volume</other>
                </relationship>
            </emdb_reference>
        </emdb_list>
    </crossreferences>
    <sample>
        <name>DNA Nanostructure</name>
        <supramolecule_list>
            <complex_supramolecule supramolecule_id="1">
                <name>DNA Nanostructure</name>
                <parent>0</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>1</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <natural_source database="NCBI">
                    <organism ncbi="32630">synthetic construct</organism>
                </natural_source>
            </complex_supramolecule>
            <complex_supramolecule supramolecule_id="2">
                <name>Scaffold DNA single-strand</name>
                <parent>1</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>1</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <natural_source database="NCBI">
                    <organism ncbi="28360">Phage M13mp18</organism>
                </natural_source>
            </complex_supramolecule>
            <complex_supramolecule supramolecule_id="3">
                <name>staple oligonucleotides</name>
                <parent>1</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>1</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <natural_source database="NCBI">
                    <organism ncbi="32630">synthetic construct</organism>
                </natural_source>
            </complex_supramolecule>
        </supramolecule_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">
                    <buffer>
                        <ph>5.0</ph>
                        <details>5 mM MES, 5mM NaCl and 5 mM MgCl2</details>
                    </buffer>
                    <grid>
                        <model>C-flat-1.2/1.3</model>
                        <material>COPPER</material>
                        <mesh>400</mesh>
                        <support_film film_type_id="1">
                            <film_material>CARBON</film_material>
                            <film_topology>HOLEY</film_topology>
                        </support_film>
                        <pretreatment>
                            <type>GLOW DISCHARGE</type>
                        </pretreatment>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">100</chamber_humidity>
                        <chamber_temperature units="K">277</chamber_temperature>
                        <instrument>FEI VITROBOT MARK IV</instrument>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>FEI TITAN KRIOS</microscope>
                    <illumination_mode>FLOOD BEAM</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>FIELD EMISSION GUN</electron_source>
                    <acceleration_voltage units="kV">300</acceleration_voltage>
                    <nominal_defocus_min units="µm">0.5</nominal_defocus_min>
                    <nominal_defocus_max units="µm">5.0</nominal_defocus_max>
                    <nominal_magnification>47000.0</nominal_magnification>
                    <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
                    <cooling_holder_cryogen>NITROGEN</cooling_holder_cryogen>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>FEI FALCON III (4k x 4k)</film_or_detector_model>
                            <detector_mode>INTEGRATING</detector_mode>
                            <digitization_details>
                                <dimensions>
                                    <width units="pixel">4096</width>
                                    <height units="pixel">4096</height>
                                </dimensions>
                            </digitization_details>
                            <average_electron_dose_per_image units="e/Å^2">50.0</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>
                <startup_model type_of_model="INSILICO MODEL">
                    <insilico_model>de-novo generated initial model</insilico_model>
                </startup_model>
                <final_reconstruction>
                    <resolution units="Å" res_type="BY AUTHOR">7.27</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <number_images_used>196250</number_images_used>
                </final_reconstruction>
                <initial_angle_assignment>
                    <type>MAXIMUM LIKELIHOOD</type>
                </initial_angle_assignment>
                <final_angle_assignment>
                    <type>MAXIMUM LIKELIHOOD</type>
                    <software_list>
                        <software>
                            <name>RELION</name>
                        </software>
                    </software_list>
                </final_angle_assignment>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="32001">
        <file>emd_16220.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>200</col>
            <row>200</row>
            <sec>200</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>200</x>
            <y>200</y>
            <z>200</z>
        </spacing>
        <cell>
            <a units="Å">560.0</a>
            <b units="Å">560.0</b>
            <c units="Å">560.0</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>-0.18008466</minimum>
            <maximum>0.48134094</maximum>
            <average>0.00080795784</average>
            <std>0.013792306</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">2.8</x>
            <y units="Å">2.8</y>
            <z units="Å">2.8</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.102</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-16220::::</label>
        <annotation_details>10 helix bundle DNA origami object
with ssDNA handles which can form triple-stranded DNA</annotation_details>
    </map>
    <interpretation>
        <half_map_list>
            <half_map format="CCP4" size_kbytes="32001">
                <file>emd_16220_half_map_2.map.gz</file>
                <symmetry>
                    <space_group>1</space_group>
                </symmetry>
                <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
                <dimensions>
                    <col>200</col>
                    <row>200</row>
                    <sec>200</sec>
                </dimensions>
                <origin>
                    <col>0</col>
                    <row>0</row>
                    <sec>0</sec>
                </origin>
                <spacing>
                    <x>200</x>
                    <y>200</y>
                    <z>200</z>
                </spacing>
                <cell>
                    <a units="Å">560.0</a>
                    <b units="Å">560.0</b>
                    <c units="Å">560.0</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>-0.03996089</minimum>
                    <maximum>0.26664126</maximum>
                    <average>0.000034509252</average>
                    <std>0.011200319</std>
                </statistics>
                <pixel_spacing>
                    <x units="Å">2.8</x>
                    <y units="Å">2.8</y>
                    <z units="Å">2.8</z>
                </pixel_spacing>
                <contour_list>
                    <contour primary="true">
                        <source>AUTHOR</source>
                    </contour>
                </contour_list>
                <label>::::EMDATABANK.org::::EMD-16220::::</label>
                <annotation_details>10 helix bundle DNA origami object
with ssDNA handles which can form triple-stranded DNA /
half map 2</annotation_details>
            </half_map>
            <half_map format="CCP4" size_kbytes="32001">
                <file>emd_16220_half_map_1.map.gz</file>
                <symmetry>
                    <space_group>1</space_group>
                </symmetry>
                <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
                <dimensions>
                    <col>200</col>
                    <row>200</row>
                    <sec>200</sec>
                </dimensions>
                <origin>
                    <col>0</col>
                    <row>0</row>
                    <sec>0</sec>
                </origin>
                <spacing>
                    <x>200</x>
                    <y>200</y>
                    <z>200</z>
                </spacing>
                <cell>
                    <a units="Å">560.0</a>
                    <b units="Å">560.0</b>
                    <c units="Å">560.0</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>-0.03932252</minimum>
                    <maximum>0.26666504</maximum>
                    <average>0.00003768544</average>
                    <std>0.011203436</std>
                </statistics>
                <pixel_spacing>
                    <x units="Å">2.8</x>
                    <y units="Å">2.8</y>
                    <z units="Å">2.8</z>
                </pixel_spacing>
                <contour_list>
                    <contour primary="true">
                        <source>AUTHOR</source>
                    </contour>
                </contour_list>
                <label>::::EMDATABANK.org::::EMD-16220::::</label>
                <annotation_details>10 helix bundle DNA origami object
with ssDNA handles which can form triple-stranded DNA /
half map 1</annotation_details>
            </half_map>
        </half_map_list>
    </interpretation>
</emd>
