<emd emdb_id="EMD-5947" 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>2014-04-16</deposition>
            <header_release>2014-07-30</header_release>
            <map_release>2014-07-30</map_release>
            <update>2014-08-27</update>
        </key_dates>
        <title>Bacteriophage CUS-3 capsid icosahedral reconstruction</title>
        <authors_list>
            <author>Parent KN</author>
            <author>Tang J</author>
            <author>Cardone G</author>
            <author>Gilcrease EB</author>
            <author>Janssen ME</author>
            <author>Olson NH</author>
            <author>Casjens SR</author>
            <author>Baker TS</author>
        </authors_list>
        <keywords>mature virion, capsid only, icosahedrally averaged</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Parent KN</author>
                    <author order="2">Tang J</author>
                    <author order="3">Cardone G</author>
                    <author order="4">Gilcrease EB</author>
                    <author order="5">Janssen ME</author>
                    <author order="6">Olson NH</author>
                    <author order="7">Casjens SR</author>
                    <author order="8">Baker TS</author>
                    <title>Three-dimensional reconstructions of the bacteriophage CUS-3 virion reveal a conserved coat protein I-domain but a distinct tail spike receptor-binding domain</title>
                    <journal>VIROLOGY</journal>
                    <volume>464</volume>
                    <first_page>55</first_page>
                    <last_page>66</last_page>
                    <year>2014</year>
                    <external_references type="PUBMED">25043589</external_references>
                    <external_references type="DOI">doi:10.1016/j.virol.2014.06.017</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>CUS-3 virion, icosahedrally averaged</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>CUS-3 virion, icosahedrally averaged</name>
                <oligomeric_state>icosahedral</oligomeric_state>
                <number_unique_components>1</number_unique_components>
            </sample_supramolecule>
            <virus_supramolecule supramolecule_id="1">
                <name>Enterobacteria phage CUS-3</name>
                <sci_species_name ncbi="539221">Enterobacteria phage CUS-3</sci_species_name>
                <natural_host database="NCBI">
                    <organism ncbi="562">Escherichia coli</organism>
                    <strain>K1</strain>
                    <synonym_organism>BACTERIA(EUBACTERIA)</synonym_organism>
                </natural_host>
                <host_system database="NCBI" />
                <virus_shell shell_id="1">
                    <name>capsid</name>
                    <diameter units="&#8491;">690</diameter>
                    <triangulation>7</triangulation>
                </virus_shell>
                <virus_type>VIRION</virus_type>
                <virus_isolate>SPECIES</virus_isolate>
                <virus_enveloped>false</virus_enveloped>
                <virus_empty>false</virus_empty>
            </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>7.6</ph>
                        <details>10 mM Tris, 10 mM MgCl2</details>
                    </buffer>
                    <grid>
                        <details>400 mesh R2/2 Quantifoil, glow discharged</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">100</chamber_humidity>
                        <chamber_temperature units="K">90</chamber_temperature>
                        <instrument>HOMEMADE PLUNGER</instrument>
                        <method>Blot for 5 sec before plunging.</method>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>FEI POLARA 300</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">2.3</nominal_cs>
                    <nominal_defocus_min units="&#181;m">0.6</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">4.08</nominal_defocus_max>
                    <nominal_magnification>31000.0</nominal_magnification>
                    <specimen_holder_model>OTHER</specimen_holder_model>
                    <temperature>
                        <temperature_min units="K">89</temperature_min>
                        <temperature_max units="K">91</temperature_max>
                        <temperature_average units="K">90</temperature_average>
                    </temperature>
                    <alignment_procedure>
                        <legacy>
                            <astigmatism>Objective lens astigmatism was corrected at the magnification used to collect data.</astigmatism>
                        </legacy>
                    </alignment_procedure>
                    <date>2013-09-01</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">DIRECT ELECTRON DE-12 (4k x 3k)</film_or_detector_model>
                            <digitization_details>
                                <sampling_interval units="&#181;m">6</sampling_interval>
                            </digitization_details>
                            <number_real_images>419</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">23</average_electron_dose_per_image>
                            <details>The data were collected on the DE12 camera under control of the automated acquisition software, LEGINON.</details>
                        </image_recording>
                    </image_recording_list>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <details>Auto3dem was used for refinement.</details>
                <ctf_correction>
                    <details>each micrograph</details>
                </ctf_correction>
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">6.8</resolution>
                    <resolution_method>OTHER</resolution_method>
                    <software_list>
                        <software>
                            <name>Auto3dem, RobEM, autopp</name>
                        </software>
                    </software_list>
                    <details>28 frames total were collected for each image (35 e-/A2 total dose). Only 15 were used in the final reconstruction (18e-/A2 dose).</details>
                    <number_images_used>7766</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="2007511">
        <file>emd_5947.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>801</col>
            <row>801</row>
            <sec>801</sec>
        </dimensions>
        <origin>
            <col>-400</col>
            <row>-400</row>
            <sec>-400</sec>
        </origin>
        <spacing>
            <x>801</x>
            <y>801</y>
            <z>801</z>
        </spacing>
        <cell>
            <a units="&#8491;">1081.35</a>
            <b units="&#8491;">1081.35</b>
            <c units="&#8491;">1081.35</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>-15582.0</minimum>
            <maximum>32443.0</maximum>
            <average>-116.158798219999994</average>
            <std>2034.53149413999995</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">1.35</x>
            <y units="&#8491;">1.35</y>
            <z units="&#8491;">1.35</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>8240.0</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Bacteriophage CUS-3 capsid icosahedral reconstruction</annotation_details>
        <details>::::EMDATABANK.org::::EMD-5947::::</details>
    </map>
    <interpretation>
        <figure_list>
            <figure>
                <file>emd_5947.png</file>
            </figure>
        </figure_list>
    </interpretation>
</emd>