<?xml version="1.0" encoding="UTF-8"?>
<emd emdb_id="EMD-2371" version="3.0.1.9">
    <admin>
        <status_history_list>
            <status status_id="1">
                <code>HPUB</code>
            </status>
        </status_history_list>
        <current_status>
            <code>OBS</code>
            <processing_site>PDBe</processing_site>
        </current_status>
        <sites>
            <deposition>PDBe</deposition>
            <last_processing>PDBe</last_processing>
        </sites>
        <key_dates>
            <deposition>2013-05-08</deposition>
            <header_release>2013-06-05</header_release>
            <obsolete>2014-05-21</obsolete>
            <update>2014-05-21</update>
        </key_dates>
        <title>Electron cryo-microscopy of marine virus Syn.</title>
        <authors_list>
            <author>Gipson P</author>
            <author>Baker ML</author>
            <author>Liu X</author>
            <author>Raytcheva D</author>
            <author>Haase C</author>
            <author>Piret J</author>
            <author>King J</author>
            <author>Chiu W</author>
        </authors_list>
        <keywords>Syn5, marine virus, Synechococcus, cyanophage, cyanobacteria, outer capsid protein, maturation</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="false">
                    <author order="1">Gipson P</author>
                    <author order="2">Baker ML</author>
                    <author order="3">Liu X</author>
                    <author order="4">Raytcheva D</author>
                    <author order="5">Haase C</author>
                    <author order="6">Piret J</author>
                    <author order="7">King J</author>
                    <author order="8">Chiu W</author>
                    <title>A distinct structural arrangement obtained by an ancient marine virus during maturation</title>
                    <journal>To Be Published</journal>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>4bml</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>Mature capsid of marine virus Syn5</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Mature capsid of marine virus Syn5</name>
                <number_unique_components>1</number_unique_components>
            </sample_supramolecule>
            <virus_supramolecule supramolecule_id="1">
                <name synonym="horned virus">Synechococcus phage Syn5</name>
                <sci_species_name ncbi="438482">Synechococcus phage Syn5</sci_species_name>
                <natural_host database="NCBI">
                    <organism ncbi="166314">Synechococcus sp. WH 8109</organism>
                    <strain>WH 8109</strain>
                    <synonym_organism>BACTERIA(EUBACTERIA)</synonym_organism>
                </natural_host>
                <host_system database="NCBI"/>
                <virus_shell shell_id="1">
                    <diameter units="Å">640</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>
                <syn_species_name>horned virus</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">
                    <grid>
                        <details>400 mesh Cu grid R1.2/1.3 grids</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">90</chamber_humidity>
                        <instrument>FEI VITROBOT MARK IV</instrument>
                        <method>Blot for 1 second before plunging.</method>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>JEOL 3200FSC</microscope>
                    <illumination_mode>FLOOD BEAM</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">4.1</nominal_cs>
                    <nominal_defocus_min units="µm">0.0007</nominal_defocus_min>
                    <nominal_defocus_max units="µm">0.0035</nominal_defocus_max>
                    <nominal_magnification>80000.0</nominal_magnification>
                    <specimen_holder_model>JEOL 3200FSC CRYOHOLDER</specimen_holder_model>
                    <specialist_optics>
                        <energy_filter>
                            <name>Omega</name>
                            <lower_energy_threshold units="eV">0.0</lower_energy_threshold>
                            <upper_energy_threshold units="eV">25.0</upper_energy_threshold>
                        </energy_filter>
                    </specialist_optics>
                    <date>2010-08-28</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">GATAN ULTRASCAN 10000 (10k x 10k)</film_or_detector_model>
                            <number_real_images>1000</number_real_images>
                            <average_electron_dose_per_image units="e/Å^2">23</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <details>The particles were selected using EMAN2, while 3D reconstruction was performed by multi-path simulated annealing (MPSA) program.</details>
                <ctf_correction>
                    <details>each frame</details>
                </ctf_correction>
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <resolution units="Å" res_type="BY AUTHOR">5.7</resolution>
                    <resolution_method>OTHER</resolution_method>
                    <software_list>
                        <software>
                            <name>Multi-path, Simulated, Annealing, (MPSA)</name>
                        </software>
                    </software_list>
                    <number_images_used>9700</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="628865">
        <file>emd_2371.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>544</col>
            <row>544</row>
            <sec>544</sec>
        </dimensions>
        <origin>
            <col>-272</col>
            <row>-272</row>
            <sec>-272</sec>
        </origin>
        <spacing>
            <x>544</x>
            <y>544</y>
            <z>544</z>
        </spacing>
        <cell>
            <a units="Å">718.08</a>
            <b units="Å">718.08</b>
            <c units="Å">718.08</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>-0.7027967</minimum>
            <maximum>1.066728</maximum>
            <average>0.01083561</average>
            <std>0.06751607</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">1.32</x>
            <y units="Å">1.32</y>
            <z units="Å">1.32</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.26</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Reconstruction of icosahedral symmetric map of marine virus Syn5</annotation_details>
        <details>::::EMDATABANK.org::::EMD-2371::::</details>
    </map>
    <interpretation>
        <figure_list>
            <figure>
                <file>emd_2371.png</file>
            </figure>
            <figure>
                <file>emd_2371_1.png</file>
            </figure>
        </figure_list>
    </interpretation>
</emd>
