<emd emdb_id="EMD-5356" 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>2011-11-28</deposition>
            <header_release>2012-05-23</header_release>
            <map_release>2012-05-23</map_release>
            <update>2012-05-23</update>
        </key_dates>
        <title>Expansion Intermediates of the Bacteriophage phi6 Procapsid</title>
        <authors_list>
            <author>Nemecek D</author>
            <author>Cheng N</author>
            <author>Qiao J</author>
            <author>Mindich L</author>
            <author>Steven AC</author>
            <author>Heymann JB</author>
        </authors_list>
        <keywords>dsRNA virus, Cystoviridae, capsid, expansion intermediate, segmented genome</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Nemecek D</author>
                    <author order="2">Cheng N</author>
                    <author order="3">Qiao J</author>
                    <author order="4">Mindich L</author>
                    <author order="5">Steven AC</author>
                    <author order="6">Heymann JB</author>
                    <title>Stepwise Expansion of the Bacteriophage phi6 Procapsid: Possible Packaging Intermediates</title>
                    <journal>J.MOL.BIOL.</journal>
                    <volume>414</volume>
                    <first_page>260</first_page>
                    <last_page>271</last_page>
                    <year>2011</year>
                    <external_references type="PUBMED">22019738</external_references>
                    <external_references type="DOI">doi:10.1016/j.jmb.2011.10.004</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>Expansion Intermediate 2 of the P1247 Procapsid of Bacteriophage phi6</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Expansion Intermediate 2 of the P1247 Procapsid of Bacteriophage phi6</name>
                <oligomeric_state>Icosahedral shell of P1 dimers with P2, P4 and P7 subunits</oligomeric_state>
                <number_unique_components>4</number_unique_components>
                <molecular_weight>
                    <theoretical units="MDa">12.6</theoretical>
                </molecular_weight>
            </sample_supramolecule>
            <virus_supramolecule supramolecule_id="1">
                <name synonym="Bacteriophage phi6">Bacteriophage phi6</name>
                <sci_species_name>Bacteriophage phi6</sci_species_name>
                <natural_host database="NCBI">
                    <organism ncbi="317">Pseudomonas syringae</organism>
                    <synonym_organism>BACTERIA(EUBACTERIA)</synonym_organism>
                </natural_host>
                <host_system database="NCBI" />
                <molecular_weight>
                    <theoretical units="MDa">12.6</theoretical>
                </molecular_weight>
                <virus_shell shell_id="1">
                    <name>P1</name>
                    <diameter units="&#8491;">420</diameter>
                    <triangulation>1</triangulation>
                </virus_shell>
                <virus_type>OTHER</virus_type>
                <virus_isolate>STRAIN</virus_isolate>
                <virus_enveloped>true</virus_enveloped>
                <virus_empty>true</virus_empty>
                <syn_species_name>Bacteriophage phi6</syn_species_name>
            </virus_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">10</concentration>
                    <buffer>
                        <ph>7.5</ph>
                        <details>10 mM potassium phosphate, 1 mM MgCl2, 100 mM NaCl</details>
                    </buffer>
                    <grid>
                        <details>Quantifoil 2/2/400 mesh grid</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">80</chamber_humidity>
                        <chamber_temperature units="K">93</chamber_temperature>
                        <instrument>LEICA KF80</instrument>
                        <details>Vitrification instrument: Reichert - Jung KF80</details>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>FEI/PHILIPS CM200FEG</microscope>
                    <illumination_mode>FLOOD BEAM</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>FIELD EMISSION GUN</electron_source>
                    <acceleration_voltage units="kV">120</acceleration_voltage>
                    <nominal_cs units="mm">2.0</nominal_cs>
                    <nominal_defocus_min units="&#181;m">0.7</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">2.1</nominal_defocus_max>
                    <nominal_magnification>50000.0</nominal_magnification>
                    <calibrated_magnification>48327.0</calibrated_magnification>
                    <specimen_holder_model>GATAN LIQUID NITROGEN</specimen_holder_model>
                    <temperature>
                        <temperature_average units="K">93</temperature_average>
                    </temperature>
                    <alignment_procedure>
                        <legacy>
                            <astigmatism>objective lens astigmatism was corrected at 100,000 times magnification</astigmatism>
                        </legacy>
                    </alignment_procedure>
                    <date>2008-09-23</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>52</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">15</average_electron_dose_per_image>
                            <bits_per_pixel>16.</bits_per_pixel>
                        </image_recording>
                    </image_recording_list>
                    <specimen_holder>Gatan 626</specimen_holder>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <details>class 2 of 3 from multi-reference alignment</details>
                <ctf_correction>
                    <details>phase flip particle images</details>
                </ctf_correction>
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">20.0</resolution>
                    <resolution_method>FSC 0.33 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>Bsoft</name>
                        </software>
                    </software_list>
                    <number_images_used>558</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="68658">
        <file>emd_5356.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>260</col>
            <row>260</row>
            <sec>260</sec>
        </dimensions>
        <origin>
            <col>-130</col>
            <row>-130</row>
            <sec>-130</sec>
        </origin>
        <spacing>
            <x>260</x>
            <y>260</y>
            <z>260</z>
        </spacing>
        <cell>
            <a units="&#8491;">683.25916</a>
            <b units="&#8491;">683.25916</b>
            <c units="&#8491;">683.25916</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>-4.86563253</minimum>
            <maximum>6.11769676</maximum>
            <average>0.0</average>
            <std>1.0</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">2.62792</x>
            <y units="&#8491;">2.62792</y>
            <z units="&#8491;">2.62792</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>1.62</level>
                <source>EMDB</source>
            </contour>
        </contour_list>
        <annotation_details>This is expansion intermediate of the bacteriophage phi6 procapsid that was obtained by RNA release from already packaged capsids.</annotation_details>
        <details>::::EMDATABANK.org::::EMD-5356::::</details>
    </map>
    <validation>
        <fsc_curve>
            <file>emd_5356_fsc.xml</file>
        </fsc_curve>
    </validation>
</emd>