<emd emdb_id="EMD-5113" 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>2009-03-16</deposition>
            <header_release>2009-05-15</header_release>
            <map_release>2009-05-15</map_release>
            <update>2014-04-16</update>
        </key_dates>
        <title>The Structure of Leishmania Mitochondrial Ribosome with Minimal RNA.</title>
        <authors_list>
            <author>Sharma MR</author>
            <author>Booth TM</author>
            <author>Simpson L</author>
            <author>Maslov DA</author>
            <author>Agrawal RK</author>
        </authors_list>
        <keywords>Leishmania tarentolae, Mitochondrial ribosome, CryoEM, Minimal RNA.</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Sharma MR</author>
                    <author order="2">Booth TM</author>
                    <author order="3">Simpson L</author>
                    <author order="4">Maslov DA</author>
                    <author order="5">Agrawal RK</author>
                    <title>Structure of a mitochondrial ribosome with minimal RNA.</title>
                    <journal>PROC.NAT.ACAD.SCI.USA</journal>
                    <volume>106</volume>
                    <first_page>9637</first_page>
                    <last_page>9642</last_page>
                    <year>2009</year>
                    <external_references type="PUBMED">19497863</external_references>
                    <external_references type="DOI">doi:10.1073/pnas.0901631106</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>3iy8</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
            <pdb_reference>
                <pdb_id>3iy9</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>Leishmania Mitochondrial 50S Ribosome</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Leishmania Mitochondrial 50S Ribosome</name>
                <oligomeric_state>Monomer</oligomeric_state>
                <number_unique_components>1</number_unique_components>
                <molecular_weight>
                    <experimental units="MDa">2.1</experimental>
                    <method>Proteomics</method>
                </molecular_weight>
            </sample_supramolecule>
            <complex_supramolecule supramolecule_id="1">
                <name>50S Ribosome</name>
                <recombinant_exp_flag>false</recombinant_exp_flag>
                <natural_source database="NCBI">
                    <organism ncbi="5689">Leishmania tarentolae</organism>
                    <organelle>mitochondrion</organelle>
                </natural_source>
                <recombinant_expression database="NCBI" />
                <molecular_weight>
                    <experimental units="MDa">2.1</experimental>
                </molecular_weight>
                <ribosome-details>ribosome-prokaryote: LSU 50S</ribosome-details>
            </complex_supramolecule>
        </supramolecule_list>
    </sample>
    <structure_determination_list>
        <structure_determination structure_determination_id="1">
            <method>singleParticle</method>
            <aggregation_state>particle</aggregation_state>
            <specimen_preparation_list>
                <single_particle_preparation preparation_id="1">
                    <concentration units="mg/mL">0.067</concentration>
                    <buffer>
                        <ph>7.5</ph>
                        <details>50 mM Tris-HCl, pH 7.5, 100 mM KCl, 10 mM MgCl2, 3 mM DTT, 0.1 mM EDTA and 0.05% dodecyl maltoside</details>
                    </buffer>
                    <staining>
                        <type>NEGATIVE</type>
                        <details>Cryo EM</details>
                    </staining>
                    <grid>
                        <details>300 copper Mesh grid</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">90</chamber_humidity>
                        <instrument>OTHER</instrument>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>FEI TECNAI F20</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_defocus_min units="&#181;m">1.6</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">4.5</nominal_defocus_max>
                    <nominal_magnification>50000.0</nominal_magnification>
                    <calibrated_magnification>50760.0</calibrated_magnification>
                    <specimen_holder_model>OTHER</specimen_holder_model>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="FILM">KODAK SO-163 FILM</film_or_detector_model>
                            <digitization_details>
                                <scanner>ZEISS SCAI</scanner>
                                <sampling_interval units="&#181;m">14</sampling_interval>
                            </digitization_details>
                            <number_real_images>267</number_real_images>
                            <bits_per_pixel>12.</bits_per_pixel>
                        </image_recording>
                    </image_recording_list>
                    <specimen_holder>eucentric</specimen_holder>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <ctf_correction>
                    <details>Each Micrograph</details>
                </ctf_correction>
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">14.1</resolution>
                    <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>SPIDER</name>
                        </software>
                    </software_list>
                    <number_images_used>53475</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="8584">
        <file>emd_5113.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>130</col>
            <row>130</row>
            <sec>130</sec>
        </dimensions>
        <origin>
            <col>-65</col>
            <row>-65</row>
            <sec>-65</sec>
        </origin>
        <spacing>
            <x>130</x>
            <y>130</y>
            <z>130</z>
        </spacing>
        <cell>
            <a units="&#8491;">358.8</a>
            <b units="&#8491;">358.8</b>
            <c units="&#8491;">358.8</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>-0.00191628</minimum>
            <maximum>0.00403481</maximum>
            <average>0.00008317</average>
            <std>0.00023827</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">2.76</x>
            <y units="&#8491;">2.76</y>
            <z units="&#8491;">2.76</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.00055</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Leishmania mitoribosome</annotation_details>
        <details>::::EMDATABANK.org::::EMD-5113::::</details>
    </map>
</emd>