<emd emdb_id="EMD-1697" 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>PDBe</processing_site>
        </current_status>
        <sites>
            <deposition>PDBe</deposition>
            <last_processing>PDBe</last_processing>
        </sites>
        <key_dates>
            <deposition>2010-01-26</deposition>
            <header_release>2010-05-13</header_release>
            <map_release>2010-05-13</map_release>
            <update>2011-09-09</update>
        </key_dates>
        <title>Outer dynein arms with a microtubule doublet in the presence of ADP.Vanadate</title>
        <authors_list>
            <author>Movassagh T</author>
            <author>Bui KH</author>
            <author>Sakakibara H</author>
            <author>Oiwa K</author>
            <author>Ishikawa T</author>
        </authors_list>
        <keywords>Dynein,flagella,ATP,tomography,motility,tubulin,microtubule</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Movassagh T</author>
                    <author order="2">Bui KH</author>
                    <author order="3">Sakakibara H</author>
                    <author order="4">Oiwa K</author>
                    <author order="5">Ishikawa T</author>
                    <title>Nucleotide-induced global conformational changes of flagellar dynein arms revealed by in situ analysis.</title>
                    <journal>NAT.STRUCT.MOL.BIOL.</journal>
                    <volume>17</volume>
                    <first_page>761</first_page>
                    <last_page>767</last_page>
                    <year>2010</year>
                    <external_references type="PUBMED">20453857</external_references>
                    <external_references type="DOI">doi:10.1038/nsmb.1832</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>Outer dynein arm, microtubule doublet</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Outer dynein arm, microtubule doublet</name>
                <details>The sample was flagella in situ</details>
                <number_unique_components>1</number_unique_components>
            </sample_supramolecule>
            <organelle_or_cellular_component_supramolecule supramolecule_id="1">
                <name synonym="Outer dynein arm and Microtubule doublet">Flagella</name>
                <recombinant_exp_flag>false</recombinant_exp_flag>
                <natural_source database="NCBI">
                    <organism ncbi="3055">Chlamydomonas reinhardtii</organism>
                    <synonym_organism>Green Algae</synonym_organism>
                    <organelle>Flagella</organelle>
                    <cellular_location>Axoneme</cellular_location>
                </natural_source>
                <recombinant_expression database="NCBI" />
            </organelle_or_cellular_component_supramolecule>
        </supramolecule_list>
    </sample>
    <structure_determination_list>
        <structure_determination structure_determination_id="1">
            <method>subtomogramAveraging</method>
            <aggregation_state>particle</aggregation_state>
            <specimen_preparation_list>
                <subtomogram_averaging_preparation preparation_id="1">
                    <buffer>
                        <ph>7.4</ph>
                        <details>30 mM HEPES (pH 7.4), 5 mM MgSO4, 1 mM DTT, 1 mM EGTA, 50 mM Potassium Acetate, 0.5% (w/v) Polyethylene Glycol (MW 20,000), 0.1 mM ATP with 0.05 mM sodium Orthovanadate</details>
                    </buffer>
                    <grid>
                        <details>300 mesh lacey carbon grid</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">95</chamber_humidity>
                        <instrument>OTHER</instrument>
                        <details>Vitrification instrument: Vitrobot</details>
                        <method>Blot for 3 seconds before plunging</method>
                    </vitrification>
                </subtomogram_averaging_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <subtomogram_averaging_microscopy microscopy_id="1">
                    <microscope>FEI TECNAI 20</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>
                    <specimen_holder_model>GATAN LIQUID NITROGEN</specimen_holder_model>
                    <temperature>
                        <temperature_average units="K">100</temperature_average>
                    </temperature>
                    <specialist_optics>
                        <energy_filter>
                            <name>GIF</name>
                            <lower_energy_threshold units="eV">10.0</lower_energy_threshold>
                            <upper_energy_threshold units="eV">25.0</upper_energy_threshold>
                        </energy_filter>
                    </specialist_optics>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">GENERIC GATAN</film_or_detector_model>
                            <digitization_details>
                                <sampling_interval units="&#181;m">6.85</sampling_interval>
                            </digitization_details>
                            <number_real_images>1200</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">30</average_electron_dose_per_image>
                            <bits_per_pixel>16.</bits_per_pixel>
                        </image_recording>
                    </image_recording_list>
                    <specimen_holder>Eucentric Gatan cryo</specimen_holder>
                    <tilt_series>
                        <axis1>
                            <min_angle units="deg">-60</min_angle>
                            <max_angle units="deg">60</max_angle>
                        </axis1>
                    </tilt_series>
                </subtomogram_averaging_microscopy>
            </microscopy_list>
            <subtomogram_averaging_processing image_processing_id="1">
                <details>Average number of projections used in the 3D reconstructions: 6097. Average number of class averages: 2.</details>
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">39.0</resolution>
                    <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>IMOD</name>
                        </software>
                    </software_list>
                </final_reconstruction>
            </subtomogram_averaging_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="3187">
        <file>emd_1697.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>118</col>
            <row>128</row>
            <sec>54</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>128</x>
            <y>118</y>
            <z>54</z>
        </spacing>
        <cell>
            <a units="&#8491;">876.8</a>
            <b units="&#8491;">808.3</b>
            <c units="&#8491;">369.9</c>
            <alpha units="deg">90</alpha>
            <beta units="deg">90</beta>
            <gamma units="deg">90</gamma>
        </cell>
        <axis_order>
            <fast>X</fast>
            <medium>Y</medium>
            <slow>Z</slow>
        </axis_order>
        <statistics>
            <minimum>-5.70157</minimum>
            <maximum>9.42592</maximum>
            <average>0.246369</average>
            <std>1.69908</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">6.85</x>
            <y units="&#8491;">6.85</y>
            <z units="&#8491;">6.85</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.0</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>This is an image of outer dynein arms with a microtubule doublet in the presence of ADP.Vanadate</annotation_details>
        <details>::::EMDATABANK.org::::EMD-1697::::</details>
    </map>
</emd>