<emd emdb_id="EMD-1990" 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>2011-11-14</deposition>
            <header_release>2012-08-01</header_release>
            <map_release>2012-08-01</map_release>
            <update>2012-08-01</update>
        </key_dates>
        <title>Structure of bare F-actin filaments obtained from the same sample as the Actin-Tropomyosin-Myosin Complex</title>
        <authors_list>
            <author>Behrmann E</author>
            <author>Mueller M</author>
            <author>Penczek PA</author>
            <author>Mannherz HG</author>
            <author>Manstein DJ</author>
            <author>Raunser S</author>
        </authors_list>
        <keywords>Structural protein,cytoskeleton,myosin binding, actin binding</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Behrmann E</author>
                    <author order="2">Mueller M</author>
                    <author order="3">Penczek PA</author>
                    <author order="4">Mannherz HG</author>
                    <author order="5">Manstein DJ</author>
                    <author order="6">Raunser S</author>
                    <title>Structure of the rigor actin-tropomyosin-myosin complex.</title>
                    <journal>CELL(CAMBRIDGE,MASS.)</journal>
                    <volume>150</volume>
                    <first_page>327</first_page>
                    <last_page>338</last_page>
                    <year>2012</year>
                    <external_references type="PUBMED">22817895</external_references>
                    <external_references type="DOI">doi:10.1016/j.cell.2012.05.037</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>4a7n</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>Bare F-actin filaments</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Bare F-actin filaments</name>
                <number_unique_components>1</number_unique_components>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name synonym="actin filament">F-actin</name>
                <natural_source database="NCBI">
                    <organism ncbi="9986">Oryctolagus cuniculus</organism>
                    <synonym_organism>Rabbit</synonym_organism>
                    <tissue>skeletal muscle</tissue>
                    <organelle>Sarcoplasm</organelle>
                    <cellular_location>Sarcoplasm</cellular_location>
                </natural_source>
                <number_of_copies>14</number_of_copies>
                <oligomeric_state>filament</oligomeric_state>
                <recombinant_exp_flag>false</recombinant_exp_flag>
                <recombinant_expression database="NCBI" />
                <sequence>
                    <external_references type="GO">GO:0042643</external_references>
                    <external_references type="INTERPRO">IPR004000</external_references>
                </sequence>
            </protein_or_peptide>
        </macromolecule_list>
    </sample>
    <structure_determination_list>
        <structure_determination structure_determination_id="1">
            <method>helical</method>
            <aggregation_state>filament</aggregation_state>
            <specimen_preparation_list>
                <helical_preparation preparation_id="1">
                    <concentration units="mg/mL">0.01</concentration>
                    <buffer>
                        <ph>7.2</ph>
                        <details>5mM Tris, 100mM KCl, 2mM MgCl2, 50mM glutamine, 50mM arginine</details>
                    </buffer>
                    <grid>
                        <details>C-Flat CF-2/1-4C copper 400 mesh</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">90</chamber_humidity>
                        <chamber_temperature units="K">101</chamber_temperature>
                        <instrument>GATAN CRYOPLUNGE 3</instrument>
                        <details>Vitrification instrument: Gatan Cryoplunge 3</details>
                        <method>Manual blotting for approximately 15 seconds</method>
                    </vitrification>
                </helical_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <helical_microscopy microscopy_id="1">
                    <microscope>JEOL 3200FSC</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">4.1</nominal_cs>
                    <nominal_defocus_min units="&#181;m">0.75</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">1.5</nominal_defocus_max>
                    <nominal_magnification>80000.0</nominal_magnification>
                    <calibrated_magnification>169644.0</calibrated_magnification>
                    <specimen_holder_model>JEOL 3200FSC CRYOHOLDER</specimen_holder_model>
                    <temperature>
                        <temperature_average units="K">77</temperature_average>
                    </temperature>
                    <alignment_procedure>
                        <legacy>
                            <astigmatism>objective lens astigmatism was corrected at 150,000 times magnification</astigmatism>
                        </legacy>
                    </alignment_procedure>
                    <specialist_optics>
                        <energy_filter>
                            <name>in-column Omega filter</name>
                            <lower_energy_threshold units="eV">0.0</lower_energy_threshold>
                            <upper_energy_threshold units="eV">12.0</upper_energy_threshold>
                        </energy_filter>
                    </specialist_optics>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">TVIPS TEMCAM-F816 (8k x 8k)</film_or_detector_model>
                            <digitization_details>
                                <sampling_interval units="&#181;m">15.6</sampling_interval>
                            </digitization_details>
                            <number_real_images>836</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">17</average_electron_dose_per_image>
                            <details>Over 3000 images were taken of which only the best 836 were used for processing</details>
                            <bits_per_pixel>14.</bits_per_pixel>
                        </image_recording>
                    </image_recording_list>
                    <specimen_holder>cryogenic stage with side entry access</specimen_holder>
                </helical_microscopy>
            </microscopy_list>
            <helical_processing image_processing_id="1">
                <details>Particles were selected by hand using e2helixboxer</details>
                <final_reconstruction>
                    <applied_symmetry>
                        <helical_parameters>
                            <delta_z units="&#8491;">27.6</delta_z>
                            <delta_phi units="deg">166.5</delta_phi>
                        </helical_parameters>
                    </applied_symmetry>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">8.9</resolution>
                    <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>SPARX</name>
                        </software>
                    </software_list>
                </final_reconstruction>
                <ctf_correction>
                    <details>each particle</details>
                </ctf_correction>
            </helical_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="22001">
        <file>emd_1990.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>160</col>
            <row>160</row>
            <sec>220</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>160</x>
            <y>160</y>
            <z>220</z>
        </spacing>
        <cell>
            <a units="&#8491;">294.4</a>
            <b units="&#8491;">294.4</b>
            <c units="&#8491;">404.80002</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>0.0</minimum>
            <maximum>0.11287101</maximum>
            <average>0.00048386</average>
            <std>0.00331855</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">1.84</x>
            <y units="&#8491;">1.84</y>
            <z units="&#8491;">1.84</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.009</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>undecorated F-actin filament</annotation_details>
        <details>::::EMDATABANK.org::::EMD-1990::::</details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <initial_model>
                    <access_code>3MFP</access_code>
                </initial_model>
                <refinement_protocol>FLEXIBLE FIT</refinement_protocol>
                <software_list>
                    <software>
                        <name>DireX</name>
                    </software>
                </software_list>
                <details>Protocol: geometry-based conformational sampling using Deformable Elastic Network (DEN) approach. Initial placement was performed using rigid-body fitting in Chimera</details>
                <refinement_space>REAL</refinement_space>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>