<emd emdb_id="EMD-6471" version="3.0.1.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="https://github.com/emdb-empiar/emdb-schemas/blob/master/v3/v3_0_1_1/emdb_relaxed.xsd">
    <admin>
        <current_status>
            <code>REL</code>
            <processing_site>RCSB</processing_site>
        </current_status>
        <sites>
            <deposition>RCSB</deposition>
            <last_processing>RCSB</last_processing>
        </sites>
        <key_dates>
            <deposition>2015-09-21</deposition>
            <header_release>2015-10-21</header_release>
            <map_release>2015-11-04</map_release>
            <update>2015-11-11</update>
        </key_dates>
        <title>Platelet from a healthy woman</title>
        <authors_list>
            <author>Wang R</author>
            <author>Stone RL</author>
            <author>Kaelber JT</author>
            <author>Rochat RH</author>
            <author>Nick AM</author>
            <author>Vijayan KV</author>
            <author>Afshar-Kharghan V</author>
            <author>Schmid MF</author>
            <author>Dong JF</author>
            <author>Sood AK</author>
            <author>Chiu W</author>
        </authors_list>
        <keywords>ovarian cancer, platelet, thrombosis, ultrastructure</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Wang R</author>
                    <author order="2">Stone R</author>
                    <author order="3">Kaelber J</author>
                    <author order="4">Rochat R</author>
                    <author order="5">Nick A</author>
                    <author order="6">Vijayan K</author>
                    <author order="7">Afshar-Kharghan V</author>
                    <author order="8">Schmid M</author>
                    <author order="9">Dong JF</author>
                    <author order="10">Sood A</author>
                    <author order="11">Chiu W</author>
                    <title>Electron Cryo-tomography Reveals Ultrastructure Alterations in Platelets from Ovarian Cancer Patients</title>
                    <journal>PROC.NAT.ACAD.SCI.USA</journal>
                    <year>2015</year>
                    <external_references type="DOI">doi:10.1073/pnas.1518628112</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>Tomographic reconstruction of a platelet from a healthy donor</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Tomographic reconstruction of a platelet from a healthy donor</name>
                <number_unique_components>1</number_unique_components>
            </sample_supramolecule>
            <organelle_or_cellular_component_supramolecule supramolecule_id="1">
                <name synonym="thrombocyte">platelet</name>
                <number_of_copies>1</number_of_copies>
                <recombinant_exp_flag>false</recombinant_exp_flag>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                    <synonym_organism>human</synonym_organism>
                    <tissue>blood</tissue>
                    <cell>platelet</cell>
                </natural_source>
                <recombinant_expression database="NCBI" />
            </organelle_or_cellular_component_supramolecule>
        </supramolecule_list>
    </sample>
    <structure_determination_list>
        <structure_determination structure_determination_id="1">
            <method>tomography</method>
            <aggregation_state>cell</aggregation_state>
            <specimen_preparation_list>
                <tomography_preparation preparation_id="1">
                    <buffer>
                        <details>native platelet-rich plasma</details>
                    </buffer>
                    <grid>
                        <details>200 mesh Quantifoil R3.5/1</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">100</chamber_humidity>
                        <instrument>FEI VITROBOT MARK IV</instrument>
                        <method>2 blots, 2 seconds each</method>
                    </vitrification>
                </tomography_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <tomography_microscopy microscopy_id="1">
                    <microscope>JEOL 2200FSC</microscope>
                    <illumination_mode>FLOOD BEAM</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>FIELD EMISSION GUN</electron_source>
                    <acceleration_voltage units="kV">200</acceleration_voltage>
                    <nominal_cs units="mm">2.0</nominal_cs>
                    <nominal_defocus_max units="&#181;m">15.0</nominal_defocus_max>
                    <nominal_magnification>10000.0</nominal_magnification>
                    <calibrated_magnification>12500.0</calibrated_magnification>
                    <specimen_holder_model>GATAN LIQUID NITROGEN</specimen_holder_model>
                    <alignment_procedure>
                        <legacy>
                            <astigmatism>objective lens astigmatism correction</astigmatism>
                        </legacy>
                    </alignment_procedure>
                    <specialist_optics>
                        <energy_filter>
                            <name>omega filter</name>
                            <lower_energy_threshold units="eV">0.0</lower_energy_threshold>
                            <upper_energy_threshold units="eV">15.0</upper_energy_threshold>
                        </energy_filter>
                    </specialist_optics>
                    <details>2 degree tilt increment</details>
                    <date>2011-10-11</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">GATAN ULTRASCAN 4000 (4k x 4k)</film_or_detector_model>
                            <number_real_images>62</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">2</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                    <tilt_series>
                        <axis1>
                            <min_angle units="deg">-62</min_angle>
                            <max_angle units="deg">62</max_angle>
                            <angle_increment units="deg">2</angle_increment>
                        </axis1>
                    </tilt_series>
                </tomography_microscopy>
            </microscopy_list>
            <tomography_processing image_processing_id="1">
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <software_list>
                        <software>
                            <name>IMOD</name>
                        </software>
                    </software_list>
                    <number_images_used>62</number_images_used>
                </final_reconstruction>
            </tomography_processing>
        </structure_determination>
    </structure_determination_list>
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        <file>emd_6471.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS SIGNED BYTE</data_type>
        <dimensions>
            <col>3135</col>
            <row>3420</row>
            <sec>500</sec>
        </dimensions>
        <origin>
            <col>-896</col>
            <row>-282</row>
            <sec>200</sec>
        </origin>
        <spacing>
            <x>3420</x>
            <y>3135</y>
            <z>500</z>
        </spacing>
        <cell>
            <a units="&#8491;">37620.0</a>
            <b units="&#8491;">41040.0</b>
            <c units="&#8491;">6000.0</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>-128.0</minimum>
            <maximum>127.0</maximum>
            <average>7.05368996</average>
            <std>86.030555730000003</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">12.0</x>
            <y units="&#8491;">12.0</y>
            <z units="&#8491;">12.0</z>
        </pixel_spacing>
        <annotation_details>Tomographic reconstruction of a platelet from a healthy donor</annotation_details>
        <details>::::EMDATABANK.org::::EMD-6471::::</details>
    </map>
    <interpretation>
        <figure_list>
            <figure>
                <file>emd_6471.png</file>
            </figure>
        </figure_list>
    </interpretation>
</emd>