<emd emdb_id="EMD-5303" 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>2011-06-08</deposition>
            <header_release>2011-06-21</header_release>
            <map_release>2011-06-21</map_release>
            <update>2013-06-05</update>
        </key_dates>
        <title>Trypanosoma brucei flagellum: paraflagellar rod</title>
        <authors_list>
            <author>Koyfman AY</author>
            <author>Schmid MF</author>
            <author>Gheiratmand L</author>
            <author>Fu CJ</author>
            <author>Khant HA</author>
            <author>Huang D</author>
            <author>He CY</author>
            <author>Chiu W</author>
        </authors_list>
        <keywords>paraflagellar rod</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Koyfman AY</author>
                    <author order="2">Schmid MF</author>
                    <author order="3">Gheiratmand L</author>
                    <author order="4">Fu CJ</author>
                    <author order="5">Khant HA</author>
                    <author order="6">Huang D</author>
                    <author order="7">He CY</author>
                    <author order="8">Chiu W</author>
                    <title>Structure of Trypanosoma brucei flagellum accounts for its bihelical motion.</title>
                    <journal>PROC.NAT.ACAD.SCI.USA</journal>
                    <volume>108</volume>
                    <first_page>11105</first_page>
                    <last_page>11108</last_page>
                    <year>2011</year>
                    <external_references type="PUBMED">21690369</external_references>
                    <external_references type="DOI">doi:10.1073/pnas.1103634108</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>Trypanosoma brucei flagellum - paraflagellar rod</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Trypanosoma brucei flagellum - paraflagellar rod</name>
                <number_unique_components>1</number_unique_components>
            </sample_supramolecule>
            <organelle_or_cellular_component_supramolecule supramolecule_id="1">
                <name synonym="paraflagellar rod">paraflagellar rod</name>
                <recombinant_exp_flag>false</recombinant_exp_flag>
                <natural_source database="NCBI">
                    <organism ncbi="5691">Trypanosoma brucei</organism>
                    <synonym_organism>Trypanosome</synonym_organism>
                    <organelle>flagellum</organelle>
                    <cellular_location>flagellum</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>
            <specimen_preparation_list>
                <subtomogram_averaging_preparation preparation_id="1">
                    <buffer>
                        <details>PBS</details>
                    </buffer>
                    <grid>
                        <details>200 mesh gold grid</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">100</chamber_humidity>
                        <chamber_temperature units="K">100</chamber_temperature>
                        <instrument>FEI VITROBOT MARK III</instrument>
                        <details>Vitrification instrument: Vitrobot III</details>
                        <method>Blot for 2 seconds before plunging</method>
                    </vitrification>
                </subtomogram_averaging_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <subtomogram_averaging_microscopy microscopy_id="1">
                    <microscope>JEOL 2100</microscope>
                    <illumination_mode>FLOOD BEAM</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>LAB6</electron_source>
                    <acceleration_voltage units="kV">200</acceleration_voltage>
                    <nominal_magnification>15000.0</nominal_magnification>
                    <specimen_holder_model>GATAN LIQUID NITROGEN</specimen_holder_model>
                    <date>2008-06-25</date>
                    <image_recording_list>
                        <image_recording>
                            <average_electron_dose_per_image units="e/&#8491;^2">70</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                    <specimen_holder>60 degree</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 tilts used in the 3D reconstructions: 60. Average tomographic tilt angle increment: 2.</details>
                <final_reconstruction>
                    <software_list>
                        <software>
                            <name>IMOD</name>
                        </software>
                    </software_list>
                </final_reconstruction>
            </subtomogram_averaging_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="63135">
        <file>emd_5303.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>270</col>
            <row>205</row>
            <sec>292</sec>
        </dimensions>
        <origin>
            <col>-240</col>
            <row>58</row>
            <sec>-185</sec>
        </origin>
        <spacing>
            <x>205</x>
            <y>270</y>
            <z>292</z>
        </spacing>
        <cell>
            <a units="&#8491;">2885.22</a>
            <b units="&#8491;">2190.63</b>
            <c units="&#8491;">3120.604</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>-5.72570038</minimum>
            <maximum>7.46955013</maximum>
            <average>0.0104017</average>
            <std>0.78655183</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">10.686</x>
            <y units="&#8491;">10.686</y>
            <z units="&#8491;">10.687</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>2.5</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Sub-tomogram average of the paraflagellar rod (PFR) of Trypanosoma brucei</annotation_details>
        <details>::::EMDATABANK.org::::EMD-5303::::</details>
    </map>
</emd>