<emd emdb_id="EMD-6594" 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>2016-02-23</deposition>
            <header_release>2016-03-23</header_release>
            <map_release>2016-03-23</map_release>
            <update>2016-04-27</update>
        </key_dates>
        <title>Cryo-EM of human Ndc80-broccoli bound to microtubules</title>
        <authors_list>
            <author>Wilson-Kubalek EM</author>
            <author>Cheeseman IM</author>
            <author>Milligan RA</author>
        </authors_list>
        <keywords>Kinetochore protein complex</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Wilson-Kubalek EM</author>
                    <author order="2">Cheeseman IM</author>
                    <author order="3">Milligan RA</author>
                    <title>Structural comparison of the C. elegans and human Ndc80 complexes bound to microtubules reveals distinct binding behavior.</title>
                    <journal>MOL.BIOL.CELL</journal>
                    <volume>27</volume>
                    <first_page>1197</first_page>
                    <last_page>1203</last_page>
                    <year>2016</year>
                    <external_references type="PUBMED">26941333</external_references>
                    <external_references type="DOI">doi:10.1091/mbc.e15-12-0858</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>human Ndc80 Broccoli complex bound to microtubules</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>human Ndc80 Broccoli complex bound to microtubules</name>
                <oligomeric_state>helical</oligomeric_state>
                <number_unique_components>2</number_unique_components>
            </sample_supramolecule>
            <organelle_or_cellular_component_supramolecule supramolecule_id="1">
                <name>microtubule</name>
                <recombinant_exp_flag>false</recombinant_exp_flag>
                <natural_source database="NCBI">
                    <organism ncbi="32644">unidentified</organism>
                </natural_source>
                <recombinant_expression database="NCBI" />
            </organelle_or_cellular_component_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>Ndc80</name>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                    <synonym_organism>Human</synonym_organism>
                </natural_source>
                <oligomeric_state>helical</oligomeric_state>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="511693">Escherichia coli BL21</recombinant_organism>
                    <recombinant_plasmid>pST39</recombinant_plasmid>
                </recombinant_expression>
                <sequence />
            </protein_or_peptide>
        </macromolecule_list>
    </sample>
    <structure_determination_list>
        <structure_determination structure_determination_id="1">
            <method>helical</method>
            <aggregation_state>helicalArray</aggregation_state>
            <specimen_preparation_list>
                <helical_preparation preparation_id="1">
                    <buffer>
                        <ph>6.8</ph>
                        <details>80 mM PIPES, pH 6.8, 1 mM MgCl2, 1 mM EGTA</details>
                    </buffer>
                    <grid>
                        <details>400-mesh C-flat grids (Protochips, Inc) containing 2.0 micron holes separated by 2.0 micron spacing</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">90</chamber_humidity>
                        <chamber_temperature units="K">120</chamber_temperature>
                        <instrument>HOMEMADE PLUNGER</instrument>
                        <method>Blotted back of grid for 3 seconds.</method>
                    </vitrification>
                </helical_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <helical_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_cs units="mm">2.7</nominal_cs>
                    <nominal_defocus_min units="&#181;m">0.5</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">4.0</nominal_defocus_max>
                    <nominal_magnification>50000.0</nominal_magnification>
                    <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
                    <date>2013-10-07</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">GATAN K2 SUMMIT (4k x 4k)</film_or_detector_model>
                            <digitization_details>
                                <sampling_interval units="&#181;m">1.3</sampling_interval>
                            </digitization_details>
                            <number_real_images>838</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">40</average_electron_dose_per_image>
                            <details>Each image is an average of 30 frames.</details>
                        </image_recording>
                    </image_recording_list>
                </helical_microscopy>
            </microscopy_list>
            <helical_processing image_processing_id="1">
                <details>EMAN2 and FREALIGN IHRSR adapted for microtubules with a dimer repeat were used.</details>
                <final_reconstruction>
                    <applied_symmetry>
                        <helical_parameters>
                            <delta_z units="&#8491;">11.2</delta_z>
                            <delta_phi units="deg">23.817</delta_phi>
                            <axial_symmetry>C15</axial_symmetry>
                        </helical_parameters>
                    </applied_symmetry>
                    <resolution res_type="BY AUTHOR" units="&#8491;">4.2</resolution>
                    <resolution_method>OTHER</resolution_method>
                    <software_list>
                        <software>
                            <name>EMAN2, FREALIGN, IHRSR</name>
                        </software>
                    </software_list>
                    <details>The final map was calculated from two averaged data sets.</details>
                </final_reconstruction>
                <ctf_correction>
                    <details>CTFIND v3</details>
                </ctf_correction>
            </helical_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="28640">
        <file>emd_6594.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>257</col>
            <row>257</row>
            <sec>111</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>110</sec>
        </origin>
        <spacing>
            <x>257</x>
            <y>257</y>
            <z>111</z>
        </spacing>
        <cell>
            <a units="&#8491;">334.09998</a>
            <b units="&#8491;">334.09998</b>
            <c units="&#8491;">144.29999</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>-7.39598846</minimum>
            <maximum>13.738596920000001</maximum>
            <average>0.01343017</average>
            <std>1.17511463</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">1.3</x>
            <y units="&#8491;">1.3</y>
            <z units="&#8491;">1.2999998</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>2.8</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>3D reconstruction of the human Ndc80 broccoli complex bound to microtubules</annotation_details>
        <details>::::EMDATABANK.org::::EMD-6594::::</details>
    </map>
</emd>