<?xml version="1.0" encoding="UTF-8"?>
<emd emdb_id="EMD-28231" version="3.0.3.0">
    <admin>
        <current_status>
            <date>2023-04-12</date>
            <code>REL</code>
            <processing_site>RCSB</processing_site>
        </current_status>
        <sites>
            <deposition>RCSB</deposition>
            <last_processing>RCSB</last_processing>
        </sites>
        <key_dates>
            <deposition>2022-09-26</deposition>
            <header_release>2023-04-12</header_release>
            <map_release>2023-04-12</map_release>
            <update>2023-04-12</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)</funding_body>
                <code>GM083122</code>
                <country>United States</country>
            </grant_reference>
            <grant_reference>
                <funding_body>National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)</funding_body>
                <code>AI150715</code>
                <country>United States</country>
            </grant_reference>
            <grant_reference>
                <funding_body>Cancer Prevention and Research Institute of Texas (CPRIT)</funding_body>
                <code>RP140082</code>
                <country>United States</country>
            </grant_reference>
            <grant_reference>
                <funding_body>National Science Foundation (NSF, United States)</funding_body>
                <code>MCB1553334</code>
                <country>United States</country>
            </grant_reference>
            <grant_reference>
                <funding_body>Welch Foundation</funding_body>
                <code>I-2075-20210327</code>
                <country>United States</country>
            </grant_reference>
        </grant_support>
        <title>Subtomogram averages of the pre-conoid ring P1 and P2 from the cryo-FIB milled Neospora caninum</title>
        <authors_list>
            <author>Gui L</author>
            <author>O'Shaughnessy WJ</author>
            <author>Cai K</author>
            <author>Reetz E</author>
            <author>Reese ML</author>
            <author>Nicastro D</author>
        </authors_list>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author ORCID="0000-0002-2629-0689" order="1">Gui L</author>
                    <author ORCID="0000-0002-6868-2648" order="2">O'Shaughnessy WJ</author>
                    <author order="3">Cai K</author>
                    <author order="4">Reetz E</author>
                    <author ORCID="0000-0001-9401-9594" order="5">Reese ML</author>
                    <author ORCID="0000-0002-0122-7173" order="6">Nicastro D</author>
                    <title>Cryo-tomography reveals rigid-body motion and organization of apicomplexan invasion machinery.</title>
                    <journal_abbreviation>Nat Commun</journal_abbreviation>
                    <country>UK</country>
                    <volume>14</volume>
                    <first_page>1775</first_page>
                    <last_page>1775</last_page>
                    <year>2023</year>
                    <external_references type="PUBMED">36997532</external_references>
                    <external_references type="DOI">doi:10.1038/s41467-023-37327-w</external_references>
                    <external_references type="ISSN">2041-1723</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-28231</emdb_id>
                <relationship>
                    <other>associated EM volume</other>
                </relationship>
            </emdb_reference>
        </emdb_list>
    </crossreferences>
    <sample>
        <name>The cryo-FIB milled lamella from Neospora caninum in both protruded and retracted states</name>
        <supramolecule_list>
            <cell_supramolecule supramolecule_id="1">
                <name>The cryo-FIB milled lamella from Neospora caninum in both protruded and retracted states</name>
                <parent>0</parent>
                <natural_source database="NCBI">
                    <organism ncbi="29176">Neospora caninum</organism>
                </natural_source>
            </cell_supramolecule>
        </supramolecule_list>
    </sample>
    <structure_determination_list>
        <structure_determination structure_determination_id="1">
            <method>subtomogramAveraging</method>
            <aggregation_state>cell</aggregation_state>
            <specimen_preparation_list>
                <subtomogram_averaging_preparation preparation_id="1">
                    <buffer>
                        <ph>7.0</ph>
                    </buffer>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                    </vitrification>
                </subtomogram_averaging_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <subtomogram_averaging_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">0.2</nominal_defocus_min>
                    <nominal_defocus_max units="µm">0.8</nominal_defocus_max>
                    <specialist_optics>
                        <phase_plate>VOLTA PHASE PLATE</phase_plate>
                    </specialist_optics>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>GATAN K3 BIOQUANTUM (6k x 4k)</film_or_detector_model>
                            <average_electron_dose_per_image units="e/Å^2">1.5</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                </subtomogram_averaging_microscopy>
            </microscopy_list>
            <subtomogram_averaging_processing image_processing_id="1">
                <image_recording_id>1</image_recording_id>
                <final_reconstruction>
                    <applied_symmetry>
                        <point_group>C1</point_group>
                    </applied_symmetry>
                    <resolution units="Å" res_type="BY AUTHOR">49.0</resolution>
                    <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
                    <number_subtomograms_used>180</number_subtomograms_used>
                </final_reconstruction>
                <extraction>
                    <number_tomograms>4</number_tomograms>
                    <number_images_used>180</number_images_used>
                </extraction>
                <final_angle_assignment>
                    <type>NOT APPLICABLE</type>
                </final_angle_assignment>
            </subtomogram_averaging_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="48001">
        <file>emd_28231.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>300</sec>
        </dimensions>
        <origin>
            <col>-100</col>
            <row>-100</row>
            <sec>-50</sec>
        </origin>
        <spacing>
            <x>200</x>
            <y>200</y>
            <z>300</z>
        </spacing>
        <cell>
            <a units="Å">630.2</a>
            <b units="Å">630.2</b>
            <c units="Å">945.3</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>119.92621</minimum>
            <maximum>130.62006</maximum>
            <average>124.98547</average>
            <std>1.0374485</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">3.151</x>
            <y units="Å">3.151</y>
            <z units="Å">3.151</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>126.7</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-28231::::</label>
        <annotation_details>20-angstrom low-pass filtered EM map</annotation_details>
    </map>
    <interpretation>
        <additional_map_list>
            <additional_map format="CCP4" size_kbytes="48001">
                <file>emd_28231_additional_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>300</sec>
                </dimensions>
                <origin>
                    <col>-100</col>
                    <row>-100</row>
                    <sec>-50</sec>
                </origin>
                <spacing>
                    <x>200</x>
                    <y>200</y>
                    <z>300</z>
                </spacing>
                <cell>
                    <a units="Å">630.2</a>
                    <b units="Å">630.2</b>
                    <c units="Å">945.3</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>104.548584</minimum>
                    <maximum>146.08247</maximum>
                    <average>125.0144</average>
                    <std>3.8344738</std>
                </statistics>
                <pixel_spacing>
                    <x units="Å">3.151</x>
                    <y units="Å">3.151</y>
                    <z units="Å">3.151</z>
                </pixel_spacing>
                <contour_list>
                    <contour primary="true">
                        <source>AUTHOR</source>
                    </contour>
                </contour_list>
                <label>::::EMDATABANK.org::::EMD-28231::::</label>
                <annotation_details>Original EM map, no filter is applied</annotation_details>
            </additional_map>
        </additional_map_list>
        <half_map_list>
            <half_map format="CCP4" size_kbytes="48001">
                <file>emd_28231_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>300</sec>
                </dimensions>
                <origin>
                    <col>-100</col>
                    <row>-100</row>
                    <sec>-50</sec>
                </origin>
                <spacing>
                    <x>200</x>
                    <y>200</y>
                    <z>300</z>
                </spacing>
                <cell>
                    <a units="Å">630.2</a>
                    <b units="Å">630.2</b>
                    <c units="Å">945.3</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>97.0391</minimum>
                    <maximum>157.22003</maximum>
                    <average>124.92611</average>
                    <std>5.366271</std>
                </statistics>
                <pixel_spacing>
                    <x units="Å">3.151</x>
                    <y units="Å">3.151</y>
                    <z units="Å">3.151</z>
                </pixel_spacing>
                <contour_list>
                    <contour primary="true">
                        <source>AUTHOR</source>
                    </contour>
                </contour_list>
                <label>::::EMDATABANK.org::::EMD-28231::::</label>
            </half_map>
            <half_map format="CCP4" size_kbytes="48001">
                <file>emd_28231_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>300</sec>
                </dimensions>
                <origin>
                    <col>-100</col>
                    <row>-100</row>
                    <sec>-50</sec>
                </origin>
                <spacing>
                    <x>200</x>
                    <y>200</y>
                    <z>300</z>
                </spacing>
                <cell>
                    <a units="Å">630.2</a>
                    <b units="Å">630.2</b>
                    <c units="Å">945.3</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>97.24582</minimum>
                    <maximum>151.24973</maximum>
                    <average>125.1026</average>
                    <std>5.3104744</std>
                </statistics>
                <pixel_spacing>
                    <x units="Å">3.151</x>
                    <y units="Å">3.151</y>
                    <z units="Å">3.151</z>
                </pixel_spacing>
                <contour_list>
                    <contour primary="true">
                        <source>AUTHOR</source>
                    </contour>
                </contour_list>
                <label>::::EMDATABANK.org::::EMD-28231::::</label>
            </half_map>
        </half_map_list>
    </interpretation>
</emd>
