<emd emdb_id="EMD-5405" 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>2012-02-20</deposition>
            <header_release>2012-02-22</header_release>
            <map_release>2012-05-29</map_release>
            <update>2012-05-29</update>
        </key_dates>
        <title>Icosahedral reconstruction of bacteriophage P4 procapsid</title>
        <authors_list>
            <author>Dearborn AD</author>
            <author>Laurinmaki P</author>
            <author>Chandramouli P</author>
            <author>Rodenburg CM</author>
            <author>Wang S</author>
            <author>Butcher SJ</author>
            <author>Dokland T</author>
        </authors_list>
        <keywords>bacteriophage, P2, P4, capsid, procapsid, assembly, size determination, scaffolding protein, triangulation numbers, T=7 dextro, Sid, gpN</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Dearborn AD</author>
                    <author order="2">Laurinmaki P</author>
                    <author order="3">Chandramouli P</author>
                    <author order="4">Rodenburg CM</author>
                    <author order="5">Wang S</author>
                    <author order="6">Butcher SJ</author>
                    <author order="7">Dokland T</author>
                    <title>Structure and size determination of bacteriophage P2 and P4 procapsids: function of size responsiveness mutations.</title>
                    <journal>J.STRUCT.BIOL.</journal>
                    <volume>178</volume>
                    <first_page>215</first_page>
                    <last_page>224</last_page>
                    <year>2012</year>
                    <external_references type="PUBMED">22508104</external_references>
                    <external_references type="DOI">doi:10.1016/j.jsb.2012.04.002</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>Satellite bacteriophage P4 procapsid</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Satellite bacteriophage P4 procapsid</name>
                <oligomeric_state>240 copies of gpN and 60 copies of Sid</oligomeric_state>
                <number_unique_components>2</number_unique_components>
                <molecular_weight>
                    <theoretical units="MDa">11.268</theoretical>
                </molecular_weight>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name synonym="N*, major capsid protein">gpN</name>
                <natural_source database="NCBI">
                    <organism ncbi="562">Escherichia coli</organism>
                    <strain>BL21(DE3)</strain>
                    <synonym_organism>Escherichia coli</synonym_organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">9.648</theoretical>
                </molecular_weight>
                <oligomeric_state>icosahedral</oligomeric_state>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                    <recombinant_plasmid>pET21</recombinant_plasmid>
                </recombinant_expression>
                <sequence />
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="2">
                <name synonym="external scaffolding protein">Sid</name>
                <natural_source database="NCBI">
                    <organism ncbi="562">Escherichia coli</organism>
                    <strain>BL21(DE3)</strain>
                    <synonym_organism>E. coli</synonym_organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">1.62</theoretical>
                </molecular_weight>
                <oligomeric_state>icosahedral</oligomeric_state>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                    <recombinant_plasmid>pET21</recombinant_plasmid>
                </recombinant_expression>
                <sequence />
            </protein_or_peptide>
        </macromolecule_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">1.0</concentration>
                    <buffer>
                        <ph>8.0</ph>
                        <details>10 mM Tris-HCl, pH 8.0, 20 mM NaCl, 1 mM MgCl2</details>
                    </buffer>
                    <grid>
                        <details>200 mesh Quantifoil R2/2</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_temperature units="K">110</chamber_temperature>
                        <instrument>HOMEMADE PLUNGER</instrument>
                        <method>Blot for 2 sec before plunging</method>
                    </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_cs units="mm">2.0</nominal_cs>
                    <nominal_defocus_min units="&#181;m">0.9</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">3.0</nominal_defocus_max>
                    <nominal_magnification>50000.0</nominal_magnification>
                    <calibrated_magnification>50000.0</calibrated_magnification>
                    <specimen_holder_model>GATAN LIQUID NITROGEN</specimen_holder_model>
                    <temperature>
                        <temperature_min units="K">95</temperature_min>
                        <temperature_max units="K">99</temperature_max>
                        <temperature_average units="K">97</temperature_average>
                    </temperature>
                    <date>1999-01-01</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="FILM">KODAK SO-163 FILM</film_or_detector_model>
                            <digitization_details>
                                <scanner>OTHER</scanner>
                                <sampling_interval units="&#181;m">4.545</sampling_interval>
                            </digitization_details>
                            <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>
                </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;">8.0</resolution>
                    <resolution_method>OTHER</resolution_method>
                    <software_list>
                        <software>
                            <name>EMAN,AUTO3DEM</name>
                        </software>
                    </software_list>
                    <number_images_used>2286</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="39917">
        <file>emd_5405.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>217</col>
            <row>217</row>
            <sec>217</sec>
        </dimensions>
        <origin>
            <col>-108</col>
            <row>-108</row>
            <sec>-108</sec>
        </origin>
        <spacing>
            <x>217</x>
            <y>217</y>
            <z>217</z>
        </spacing>
        <cell>
            <a units="&#8491;">592.41003</a>
            <b units="&#8491;">592.41003</b>
            <c units="&#8491;">592.41003</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>-6.67676449</minimum>
            <maximum>11.10193157</maximum>
            <average>-0.00000002</average>
            <std>1.0</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">2.73</x>
            <y units="&#8491;">2.73</y>
            <z units="&#8491;">2.73</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>2.0</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Reconstruction of P4 procapsid</annotation_details>
        <details>::::EMDATABANK.org::::EMD-5405::::</details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <initial_model>
                    <access_code>3E8K</access_code>
                    <chain>
                        <chain_id>B</chain_id>
                    </chain>
                </initial_model>
                <refinement_protocol>RIGID BODY FIT</refinement_protocol>
                <software_list>
                    <software>
                        <name>Chimera</name>
                    </software>
                </software_list>
                <details>Protocol: Rigid body fitting of individual subsegments</details>
                <refinement_space>REAL</refinement_space>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>