<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" emdb_id="EMD-4045" version="3.0.0.0" xsi:schemaLocation="https://github.com/emdb-empiar/emdb-schemas/blob/master/v3/v3_0_0_0/emdb.xsd">
    <admin>
        <current_status>
            <date>2017-08-30</date>
            <code>REL</code>
            <processing_site>PDBe</processing_site>
        </current_status>
        <sites>
            <deposition>PDBe</deposition>
            <last_processing>PDBe</last_processing>
        </sites>
        <key_dates>
            <deposition>2016-06-30</deposition>
            <header_release>2016-07-13</header_release>
            <map_release>2016-07-13</map_release>
            <update>2017-08-30</update>
        </key_dates>
        <title>13-protofilament microtubule structure determined in situ from U2OS cell</title>
        <authors_list>
            <author>Grange M</author>
            <author>Vasishtan D</author>
            <author>Gruenewald K</author>
        </authors_list>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Grange M</author>
                    <author order="2">Vasishtan D</author>
                    <author order="3">Grunewald K</author>
                    <title>Cellular electron cryo tomography and in situ sub-volume averaging reveal the context of microtubule-based processes.</title>
                    <journal_abbreviation>J. Struct. Biol.</journal_abbreviation>
                    <country>US</country>
                    <volume>197</volume>
                    <first_page>181</first_page>
                    <last_page>190</last_page>
                    <year>2017</year>
                    <external_references type="PUBMED">27374320</external_references>
                    <external_references type="DOI">doi:10.1016/j.jsb.2016.06.024</external_references>
                    <external_references type="ISSN">1095-8657</external_references>
                    <external_references type="CSD">0803</external_references>
                    <external_references type="ASTM">JSBIEM</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-4045</emdb_id>
                <relationship>
                    <other>associated EM volume</other>
                </relationship>
            </emdb_reference>
        </emdb_list>
    </crossreferences>
    <sample>
        <name>Microtubule</name>
        <supramolecule_list>
            <cell_supramolecule supramolecule_id="1">
                <name>Microtubule</name>
                <parent>0</parent>
                <details>microtubule from U2OS</details>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                    <strain>U2OS</strain>
                    <tissue>Cell</tissue>
                </natural_source>
            </cell_supramolecule>
        </supramolecule_list>
    </sample>
    <structure_determination_list>
        <structure_determination structure_determination_id="1">
            <method>subtomogramAveraging</method>
            <aggregation_state>filament</aggregation_state>
            <specimen_preparation_list>
                <subtomogram_averaging_preparation preparation_id="1">
                    <buffer>
                        <ph>7.</ph>
                        <details>Cell</details>
                    </buffer>
                    <grid>
                        <model>C-flat 2/2 holey carbon gold supported grids (EMS)</model>
                        <material>GOLD</material>
                        <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-PROPANE</cryogen_name>
                        <chamber_humidity units="percentage">60</chamber_humidity>
                        <chamber_temperature units="K">298</chamber_temperature>
                        <instrument>HOMEMADE PLUNGER</instrument>
                        <details>Adherent cells grown on electron microscopy grid, manually blotted for 3s and plunge frozen. </details>
                    </vitrification>
                </subtomogram_averaging_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <subtomogram_averaging_microscopy microscopy_id="1">
                    <microscope>FEI POLARA 300</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_cs units="mm">2.0</nominal_cs>
                    <nominal_defocus_min units="&#181;m">5.0</nominal_defocus_min>
                    <calibrated_defocus_min units="&#181;m">5.0</calibrated_defocus_min>
                    <nominal_defocus_max units="&#181;m">5.0</nominal_defocus_max>
                    <calibrated_defocus_max units="&#181;m">5.0</calibrated_defocus_max>
                    <nominal_magnification>95000.</nominal_magnification>
                    <calibrated_magnification>21739.</calibrated_magnification>
                    <specimen_holder_model>OTHER</specimen_holder_model>
                    <cooling_holder_cryogen>NITROGEN</cooling_holder_cryogen>
                    <temperature>
                        <temperature_min units="K">77.0</temperature_min>
                        <temperature_max units="K">110.0</temperature_max>
                    </temperature>
                    <alignment_procedure>
                        <basic />
                    </alignment_procedure>
                    <specialist_optics>
                        <energy_filter>
                            <name>GIF Quantum</name>
                            <lower_energy_threshold units="eV">0</lower_energy_threshold>
                            <upper_energy_threshold units="eV">20</upper_energy_threshold>
                        </energy_filter>
                    </specialist_optics>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>GATAN K2 SUMMIT (4k x 4k)</film_or_detector_model>
                            <detector_mode>COUNTING</detector_mode>
                            <digitization_details>
                                <dimensions>
                                    <width units="pixel">3710</width>
                                    <height units="pixel">3836</height>
                                </dimensions>
                            </digitization_details>
                            <average_electron_dose_per_image units="e/&#8491;^2">2.5</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>
                    <number_classes_used>1</number_classes_used>
                    <applied_symmetry>
                        <helical_parameters>
                            <delta_z units="&#8491;">9.2</delta_z>
                            <delta_phi units="deg">27.6923</delta_phi>
                            <axial_symmetry>C13</axial_symmetry>
                        </helical_parameters>
                    </applied_symmetry>
                    <algorithm>FOURIER SPACE</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">25.0</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>PEET</name>
                            <version>1.10.0 Patch 3</version>
                        </software>
                    </software_list>
                    <number_subtomograms_used>1924</number_subtomograms_used>
                </final_reconstruction>
                <extraction>
                    <number_tomograms>1</number_tomograms>
                    <number_images_used>1924</number_images_used>
                    <software_list>
                        <software>
                            <name>IMOD</name>
                            <version>4.8.41</version>
                            <processing_details>3dmod</processing_details>
                        </software>
                    </software_list>
                </extraction>
                <ctf_correction>
                    <software_list>
                        <software>
                            <name>IMOD</name>
                            <version>4.8.41</version>
                            <processing_details>ctfplotter</processing_details>
                        </software>
                    </software_list>
                </ctf_correction>
                <final_angle_assignment>
                    <type>NOT APPLICABLE</type>
                    <software_list>
                        <software>
                            <name>PEET</name>
                            <version>1.10.0 Patch 3</version>
                        </software>
                    </software_list>
                </final_angle_assignment>
            </subtomogram_averaging_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="1494">
        <file>emd_4045.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>72</col>
            <row>72</row>
            <sec>72</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>72</x>
            <y>72</y>
            <z>72</z>
        </spacing>
        <cell>
            <a units="&#8491;">331.19998</a>
            <b units="&#8491;">331.19998</b>
            <c units="&#8491;">331.19998</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>-6.9646897</minimum>
            <maximum>6.982263</maximum>
            <average>-0.46713483</average>
            <std>2.4142387</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">4.6</x>
            <y units="&#8491;">4.6</y>
            <z units="&#8491;">4.6</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>2.</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::D_1200000637::::</label>
    </map>
</emd>