<emd emdb_id="EMD-5898" 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>2014-02-09</deposition>
            <header_release>2014-03-05</header_release>
            <map_release>2014-06-04</map_release>
            <update>2014-06-04</update>
        </key_dates>
        <title>Cryo EM density of microtubules stabilized by GMPCPP, without kinesin</title>
        <authors_list>
            <author>Alushin GM</author>
            <author>Lander GC</author>
            <author>Kellogg EH</author>
            <author>Zhang R</author>
            <author>Baker D</author>
            <author>Nogales E</author>
        </authors_list>
        <keywords>microtubule, gmpcpp</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Alushin GM</author>
                    <author order="2">Lander GC</author>
                    <author order="3">Kellogg EH</author>
                    <author order="4">Zhang R</author>
                    <author order="5">Baker D</author>
                    <author order="6">Nogales E</author>
                    <title>High resolution microtubule structures reveal the structural transitions in alpha-beta tubulin upon GTP hydrolysis.</title>
                    <journal>CELL(CAMBRIDGE,MASS.)</journal>
                    <volume>157</volume>
                    <first_page>1117</first_page>
                    <last_page>1129</last_page>
                    <year>2014</year>
                    <external_references type="PUBMED">24855948</external_references>
                    <external_references type="DOI">doi:10.1016/j.cell.2014.03.053</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>microtubule stabilized by GMPCPP, without kinesin</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>microtubule stabilized by GMPCPP, without kinesin</name>
                <number_unique_components>2</number_unique_components>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>Alpha tubulin</name>
                <natural_source database="NCBI">
                    <organism ncbi="9823">Sus scrofa</organism>
                    <synonym_organism>porcine</synonym_organism>
                    <tissue>brain</tissue>
                    <organelle>Cytoplasm</organelle>
                    <cellular_location>Cytoskeleton</cellular_location>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.055</theoretical>
                </molecular_weight>
                <oligomeric_state>heterodimer</oligomeric_state>
                <recombinant_exp_flag>false</recombinant_exp_flag>
                <recombinant_expression database="NCBI" />
                <sequence />
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="2">
                <name>Beta tubulin</name>
                <natural_source database="NCBI">
                    <organism ncbi="9823">Sus scrofa</organism>
                    <synonym_organism>porcine</synonym_organism>
                    <tissue>brain</tissue>
                    <organelle>Cytoplasm</organelle>
                    <cellular_location>Cytoskeleton</cellular_location>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.055</theoretical>
                </molecular_weight>
                <oligomeric_state>heterodimer</oligomeric_state>
                <recombinant_exp_flag>false</recombinant_exp_flag>
                <recombinant_expression database="NCBI" />
                <sequence />
            </protein_or_peptide>
        </macromolecule_list>
    </sample>
    <structure_determination_list>
        <structure_determination structure_determination_id="1">
            <method>singleParticle</method>
            <aggregation_state>helicalArray</aggregation_state>
            <specimen_preparation_list>
                <single_particle_preparation preparation_id="1">
                    <concentration units="mg/mL">0.25</concentration>
                    <buffer>
                        <ph>6.8</ph>
                        <details>80mM PIPES, 1mM EGTA, 1mM MgCl2, 1mM DTT, 0.05% Nonidet P-40</details>
                    </buffer>
                    <grid>
                        <details>400 mesh C-flat 1.2/1.3, glow discharged in Edwards carbon evaporator</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">90</chamber_humidity>
                        <chamber_temperature units="K">90.4</chamber_temperature>
                        <instrument>FEI VITROBOT MARK II</instrument>
                        <method>The grid was blotted for 2 seconds before plunging.</method>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>FEI TITAN</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">1.4</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">3.5</nominal_defocus_max>
                    <nominal_magnification>72000.0</nominal_magnification>
                    <calibrated_magnification>72000.0</calibrated_magnification>
                    <specimen_holder_model>GATAN LIQUID NITROGEN</specimen_holder_model>
                    <alignment_procedure>
                        <legacy>
                            <astigmatism>Objective lens astigmatism was corrected at 100,000 times magnifacation.</astigmatism>
                        </legacy>
                    </alignment_procedure>
                    <date>2012-07-12</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="FILM">KODAK SO-163 FILM</film_or_detector_model>
                            <digitization_details>
                                <scanner>OTHER</scanner>
                                <sampling_interval units="&#181;m">6.35</sampling_interval>
                            </digitization_details>
                            <number_real_images>43</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">25.0</average_electron_dose_per_image>
                            <bits_per_pixel>16.</bits_per_pixel>
                        </image_recording>
                    </image_recording_list>
                    <specimen_holder>Gatan 626 holder</specimen_holder>
                    <tilt_angle_min>0</tilt_angle_min>
                    <tilt_angle_max>0</tilt_angle_max>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <details>Initial alignments performed with EMAN2/SPARX, including refinement of helical parameters with the IHRSR programs of Egelman. Final alignment and reconstruction performed with FREALIGN.</details>
                <ctf_correction>
                    <details>ctftilt</details>
                </ctf_correction>
                <final_reconstruction>
                    <applied_symmetry>
                        <helical_parameters>
                            <delta_z units="&#8491;">8.9</delta_z>
                            <delta_phi units="deg">25.75</delta_phi>
                            <axial_symmetry>C1</axial_symmetry>
                        </helical_parameters>
                    </applied_symmetry>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">6.6</resolution>
                    <resolution_method>OTHER</resolution_method>
                    <software_list>
                        <software>
                            <name>FREALIGN</name>
                        </software>
                    </software_list>
                    <number_images_used>11394</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="4596">
        <file>emd_5898.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>110</col>
            <row>66</row>
            <sec>162</sec>
        </dimensions>
        <origin>
            <col>-55</col>
            <row>-33</row>
            <sec>-81</sec>
        </origin>
        <spacing>
            <x>66</x>
            <y>110</y>
            <z>162</z>
        </spacing>
        <cell>
            <a units="&#8491;">191.4</a>
            <b units="&#8491;">114.840004</b>
            <c units="&#8491;">281.88</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>-1.56888676</minimum>
            <maximum>4.92322493</maximum>
            <average>0.38193861</average>
            <std>1.5205611</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">1.7399999</x>
            <y units="&#8491;">1.74</y>
            <z units="&#8491;">1.74</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>3.2</level>
                <source>EMDB</source>
            </contour>
        </contour_list>
        <annotation_details>cryo-EM reconstruction of microtubule stabilized by GMPCPP, without kinesin</annotation_details>
        <details>::::EMDATABANK.org::::EMD-5898::::</details>
    </map>
</emd>