<emd emdb_id="EMD-5041" 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>2009-01-08</deposition>
            <header_release>2009-01-21</header_release>
            <map_release>2009-09-04</map_release>
            <update>2011-09-23</update>
        </key_dates>
        <title>Ribosome structure : Structural survey of large protein complexes in Desulfovibrio vulgaris Hildenborough (DvH)</title>
        <authors_list>
            <author>Han B-G</author>
            <author>Dong M</author>
            <author>Liu H</author>
            <author>Camp L</author>
            <author>Geller J</author>
            <author>Singer M</author>
            <author>Hazen TC</author>
            <author>Choi M</author>
            <author>Witkowska HE</author>
            <author>Ball DA</author>
            <author>Typke D</author>
            <author>Downing KH</author>
            <author>Shatsky M</author>
            <author>Brenner SE</author>
            <author>Chandonia J-M</author>
            <author>Biggin MD</author>
            <author>Glaeser RM</author>
        </authors_list>
        <keywords>Ribosome, Desulfovibrio vulgaris, DvH</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Han BG</author>
                    <author order="2">Dong M</author>
                    <author order="3">Liu H</author>
                    <author order="4">Camp L</author>
                    <author order="5">Geller J</author>
                    <author order="6">Singer M</author>
                    <author order="7">Hazen TC</author>
                    <author order="8">Choi M</author>
                    <author order="9">Witkowska HE</author>
                    <author order="10">Ball DA</author>
                    <author order="11">Typke D</author>
                    <author order="12">Downing KH</author>
                    <author order="13">Shatsky M</author>
                    <author order="14">Brenner SE</author>
                    <author order="15">Chandonia JM</author>
                    <author order="16">Biggin MD</author>
                    <author order="17">Glaeser RM</author>
                    <title>Survey of large protein complexes in D. vulgaris reveals great structural diversity.</title>
                    <journal>PROC.NAT.ACAD.SCI.USA</journal>
                    <volume>106</volume>
                    <first_page>16580</first_page>
                    <last_page>16585</last_page>
                    <year>2009</year>
                    <external_references type="PUBMED">19805340</external_references>
                    <external_references type="DOI">doi:10.1073/pnas.0813068106</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>70S ribosome from Desulfovibrio vulgaris Hildenborough</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>70S ribosome from Desulfovibrio vulgaris Hildenborough</name>
                <oligomeric_state>monomer</oligomeric_state>
                <number_unique_components>1</number_unique_components>
                <molecular_weight>
                    <experimental units="MDa">3</experimental>
                    <theoretical units="MDa">3</theoretical>
                    <method>Sedimentaion</method>
                </molecular_weight>
            </sample_supramolecule>
            <complex_supramolecule supramolecule_id="1">
                <name>Ribosome</name>
                <recombinant_exp_flag>false</recombinant_exp_flag>
                <natural_source database="NCBI">
                    <organism ncbi="881">Desulfovibrio vulgaris</organism>
                    <strain>Hildenborough</strain>
                    <synonym_organism>DvH</synonym_organism>
                </natural_source>
                <recombinant_expression database="NCBI" />
                <molecular_weight>
                    <experimental units="MDa">3</experimental>
                    <theoretical units="MDa">3</theoretical>
                </molecular_weight>
                <ribosome-details>ribosome-prokaryote: ALL</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">0.03</concentration>
                    <buffer>
                        <ph>7.5</ph>
                        <details>20mM Tris buffer with 60mM NH4Cl, 6mM MgCl2, 0.5mM EDTA and 1mM DTT</details>
                    </buffer>
                    <staining>
                        <type>NEGATIVE</type>
                        <details>Three microliter of 2% w/v uranyl acetate stain was applied to the EM grid for 1 min.</details>
                    </staining>
                    <grid>
                        <details>carbon-coated and glow-discharged 300 mesh copper grid</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>NONE</cryogen_name>
                        <instrument>OTHER</instrument>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>JEOL 4000EX</microscope>
                    <illumination_mode>FLOOD BEAM</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>FIELD EMISSION GUN</electron_source>
                    <acceleration_voltage units="kV">400</acceleration_voltage>
                    <nominal_cs units="mm">4.1</nominal_cs>
                    <nominal_defocus_min units="&#181;m">0.6</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">2.0</nominal_defocus_max>
                    <nominal_magnification>40000.0</nominal_magnification>
                    <calibrated_magnification>40000.0</calibrated_magnification>
                    <specimen_holder_model>OTHER</specimen_holder_model>
                    <temperature>
                        <temperature_average units="K">293</temperature_average>
                    </temperature>
                    <alignment_procedure>
                        <legacy>
                            <astigmatism>objective lens astigmatism was corrected at 60,000 times magnification</astigmatism>
                        </legacy>
                    </alignment_procedure>
                    <date>2008-07-08</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="FILM">KODAK SO-163 FILM</film_or_detector_model>
                            <digitization_details>
                                <scanner>NIKON SUPER COOLSCAN 9000</scanner>
                                <sampling_interval units="&#181;m">6.35</sampling_interval>
                            </digitization_details>
                            <number_real_images>85</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">17</average_electron_dose_per_image>
                            <details>The images were scanned with a resolution of 6.35 micro m per pixel and later averaged 2 fold in each direction.</details>
                            <bits_per_pixel>8.</bits_per_pixel>
                        </image_recording>
                    </image_recording_list>
                    <specimen_holder>Side entry room T</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">
                <ctf_correction>
                    <details>Each particle</details>
                </ctf_correction>
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">24.0</resolution>
                    <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>SPIDER</name>
                        </software>
                    </software_list>
                    <number_images_used>11000</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="8193">
        <file>emd_5041.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>128</col>
            <row>128</row>
            <sec>128</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>128</x>
            <y>128</y>
            <z>128</z>
        </spacing>
        <cell>
            <a units="&#8491;">406.4</a>
            <b units="&#8491;">406.4</b>
            <c units="&#8491;">406.4</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>-4.18105984</minimum>
            <maximum>11.958985330000001</maximum>
            <average>0.0</average>
            <std>0.99999976</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">3.175</x>
            <y units="&#8491;">3.175</y>
            <z units="&#8491;">3.175</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>1.48</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Ribosome structure from Desulfovibrio vulgaris Hildenborough (DvH)</annotation_details>
        <details>::::EMDATABANK.org::::EMD-5041::::</details>
    </map>
</emd>