<emd emdb_id="EMD-2244" 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>2012-12-18</deposition>
            <header_release>2012-12-26</header_release>
            <map_release>2013-02-20</map_release>
            <update>2016-04-20</update>
        </key_dates>
        <title>Cryo-electron microscopy of phirsl1 jumbo phage</title>
        <authors_list>
            <author>Effantin G</author>
            <author>Hamasaki R</author>
            <author>Kawasaki T</author>
            <author>Bacia M</author>
            <author>Moriscot C</author>
            <author>Weissenhorn W</author>
            <author>Yamada T</author>
            <author>Schoehn G</author>
        </authors_list>
        <keywords>Jumbo bacteriophage;phiRSL1; Ralstonia solanacearum; cryo-electron microscopy; icosahedral capsid; helical tail; T6SS</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Effantin G</author>
                    <author order="2">Hamasaki R</author>
                    <author order="3">Kawasaki T</author>
                    <author order="4">Bacia M</author>
                    <author order="5">Moriscot C</author>
                    <author order="6">Weissenhorn W</author>
                    <author order="7">Yamada T</author>
                    <author order="8">Schoehn G</author>
                    <title>Cryo-Electron Microscopy Three-Dimensional Structure of the Jumbo Phage PhiRSL1 Infecting the Phytopathogen Ralstonia solanacearum.</title>
                    <journal>STRUCTURE</journal>
                    <volume>21</volume>
                    <first_page>298</first_page>
                    <last_page>305</last_page>
                    <year>2013</year>
                    <external_references type="PUBMED">23394943</external_references>
                    <external_references type="DOI">doi:10.1016/j.str.2012.12.017</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>phirsl1 helical portion of the tail</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>phirsl1 helical portion of the tail</name>
                <number_unique_components>2</number_unique_components>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>Tail tube protein</name>
                <natural_source database="NCBI">
                    <organism ncbi="482058">Ralstonia phage RSL1</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.018</theoretical>
                </molecular_weight>
                <details>UNP B2ZY00</details>
                <recombinant_exp_flag>false</recombinant_exp_flag>
                <recombinant_expression database="NCBI" />
                <sequence />
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="2">
                <name>Tail sheath protein</name>
                <natural_source database="NCBI">
                    <organism ncbi="482058">Ralstonia phage RSL1</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.068</theoretical>
                </molecular_weight>
                <details>UNP B2ZXZ8</details>
                <recombinant_exp_flag>false</recombinant_exp_flag>
                <recombinant_expression database="NCBI" />
                <sequence>
                    <external_references type="INTERPRO">IPR007067</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">
                    <buffer>
                        <ph>7.5</ph>
                        <details>50 mM Tris-HCl [pH 7.5], 100 mM NaCl, 10 mM MgSO4</details>
                    </buffer>
                    <staining>
                        <type>NEGATIVE</type>
                        <details>Four microliters of the bacteriophage sample (~0.1 mg/ml) were loaded between the mica-carbon interface. The sample was stained using 2% ammonium molybdate pH 7.5 and air-dried.</details>
                    </staining>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">100</chamber_humidity>
                        <instrument>FEI VITROBOT MARK IV</instrument>
                    </vitrification>
                </helical_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <helical_microscopy microscopy_id="1">
                    <microscope>FEI POLARA 300</microscope>
                    <illumination_mode>SPOT SCAN</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">2.3</nominal_cs>
                    <nominal_defocus_min units="&#181;m">1.355</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">5.295</nominal_defocus_max>
                    <nominal_magnification>31000.0</nominal_magnification>
                    <specimen_holder_model>GATAN LIQUID NITROGEN</specimen_holder_model>
                    <alignment_procedure>
                        <legacy>
                            <astigmatism>Objective lens astigmatism was corrected at 59000</astigmatism>
                        </legacy>
                    </alignment_procedure>
                    <date>2011-02-25</date>
                    <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">7</sampling_interval>
                            </digitization_details>
                            <number_real_images>52</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">20</average_electron_dose_per_image>
                            <bits_per_pixel>8.</bits_per_pixel>
                        </image_recording>
                    </image_recording_list>
                </helical_microscopy>
            </microscopy_list>
            <helical_processing image_processing_id="1">
                <details>Projection matching was done with SPIDER. IHRSR was used for helical parameters search and application.</details>
                <final_reconstruction>
                    <applied_symmetry>
                        <helical_parameters>
                            <delta_z units="&#8491;">37.9</delta_z>
                            <delta_phi units="deg">22.04</delta_phi>
                            <axial_symmetry>C6</axial_symmetry>
                        </helical_parameters>
                    </applied_symmetry>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">9.6</resolution>
                    <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>SPIDER, IHRSR</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="6751">
        <file>emd_2244.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>120</col>
            <row>120</row>
            <sec>120</sec>
        </dimensions>
        <origin>
            <col>-3</col>
            <row>0</row>
            <sec>-5</sec>
        </origin>
        <spacing>
            <x>120</x>
            <y>120</y>
            <z>120</z>
        </spacing>
        <cell>
            <a units="&#8491;">271.2</a>
            <b units="&#8491;">271.2</b>
            <c units="&#8491;">271.2</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>-0.02692472</minimum>
            <maximum>0.0357494</maximum>
            <average>0.00069069</average>
            <std>0.00452792</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">2.26</x>
            <y units="&#8491;">2.26</y>
            <z units="&#8491;">2.26</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.007</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Reconstruction of the helical trunk of phirsl1 tail. A Bfactor of -538 has been applied to the reconstruction as well as a soft-edged mask.</annotation_details>
        <details>::::EMDATABANK.org::::EMD-2244::::</details>
    </map>
</emd>