<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" emdb_id="EMD-8558" version="3.0.0.0" xsi:schemaLocation="https://github.com/emdb-empiar/emdb-schemas/blob/master/v3/v3_0_0_0/emdb.xsd">
    <admin>
        <current_status>
            <date>2018-07-18</date>
            <code>REL</code>
            <processing_site>RCSB</processing_site>
        </current_status>
        <sites>
            <deposition>RCSB</deposition>
            <last_processing>RCSB</last_processing>
        </sites>
        <key_dates>
            <deposition>2017-01-13</deposition>
            <header_release>2017-02-08</header_release>
            <map_release>2017-04-26</map_release>
            <update>2018-07-18</update>
        </key_dates>
        <title>Negative stain reconstruction of Cas1-Cas2/3 complex of type I-F CRISPR system from Pseudomonas aeruginosa (PA14)</title>
        <authors_list>
            <author>Chowdhury S</author>
            <author>Lander GC</author>
            <author>Rollins MF</author>
            <author>Carter J</author>
            <author>Golden MS</author>
            <author>Wilkinson RA</author>
            <author>Bondy-Denomy J</author>
            <author>Wiedenheft B</author>
        </authors_list>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Rollins MF</author>
                    <author order="2">Chowdhury S</author>
                    <author order="3">Carter J</author>
                    <author order="4">Golden SM</author>
                    <author order="5">Wilkinson RA</author>
                    <author order="6">Bondy-Denomy J</author>
                    <author order="7">Lander GC</author>
                    <author order="8">Wiedenheft B</author>
                    <title>Cas1 and the Csy complex are opposing regulators of Cas2/3 nuclease activity.</title>
                    <journal_abbreviation>Proc. Natl. Acad. Sci. U.S.A.</journal_abbreviation>
                    <country>US</country>
                    <volume>114</volume>
                    <first_page>E5113</first_page>
                    <last_page>E5121</last_page>
                    <year>2017</year>
                    <external_references type="PUBMED">28438998</external_references>
                    <external_references type="DOI">doi:10.1073/pnas.1616395114</external_references>
                    <external_references type="ISSN">1091-6490</external_references>
                    <external_references type="CSD">0040</external_references>
                    <external_references type="ASTM">PNASA6</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-8558</emdb_id>
                <relationship>
                    <other>associated EM volume</other>
                </relationship>
            </emdb_reference>
        </emdb_list>
    </crossreferences>
    <sample>
        <name>Complex containing dimer of Cas2/3 protein and tetramer of Cas1 protein.</name>
        <supramolecule_list>
            <complex_supramolecule supramolecule_id="1">
                <name>Complex containing dimer of Cas2/3 protein and tetramer of Cas1 protein.</name>
                <parent>0</parent>
                <natural_source database="NCBI">
                    <organism ncbi="652611">Pseudomonas aeruginosa PA14</organism>
                </natural_source>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                    <recombinant_strain>BL21(DE3)</recombinant_strain>
                </recombinant_expression>
                <molecular_weight>
                    <theoretical units="MDa">0.386</theoretical>
                </molecular_weight>
            </complex_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">0.03</concentration>
                    <buffer>
                        <ph>7.5</ph>
                        <details>20 mM HEPES, 150 mM KCl</details>
                    </buffer>
                    <staining>
                        <type>NEGATIVE</type>
                        <material>Uranyl Formate</material>
                        <details>Sample absorbed on carbon surface was stained with 2% (w/v) Uranyl Formate solution, and finally air-dried after blotting off excess stain.</details>
                    </staining>
                    <grid>
                        <model>400 mesh Cu-Rh maxtaform grids (Electron Microscopy Sciences) that were coated with a thin layer of amorphous carbon.</model>
                        <material>COPPER/RHODIUM</material>
                        <mesh>400</mesh>
                        <support_film film_type_id="1">
                            <film_material>CARBON</film_material>
                            <film_topology>CONTINUOUS</film_topology>
                        </support_film>
                        <pretreatment>
                            <type>GLOW DISCHARGE</type>
                            <atmosphere>AIR</atmosphere>
                            <pressure units="kPa">0.02</pressure>
                        </pretreatment>
                        <details>15mA current</details>
                    </grid>
                    <details>Mono dispersed protein solution</details>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>FEI TECNAI SPIRIT</microscope>
                    <illumination_mode>FLOOD BEAM</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>LAB6</electron_source>
                    <acceleration_voltage units="kV">120</acceleration_voltage>
                    <c2_aperture_diameter units="&#181;m">100.0</c2_aperture_diameter>
                    <nominal_cs units="mm">2.7</nominal_cs>
                    <nominal_defocus_min units="&#181;m">1.0</nominal_defocus_min>
                    <calibrated_defocus_min units="&#181;m">0.99</calibrated_defocus_min>
                    <nominal_defocus_max units="&#181;m">1.0</nominal_defocus_max>
                    <calibrated_defocus_max units="&#181;m">0.99</calibrated_defocus_max>
                    <nominal_magnification>52000.</nominal_magnification>
                    <specimen_holder_model>SIDE ENTRY, EUCENTRIC</specimen_holder_model>
                    <cooling_holder_cryogen>NITROGEN</cooling_holder_cryogen>
                    <temperature>
                        <temperature_min units="K">293.0</temperature_min>
                        <temperature_max units="K">295.0</temperature_max>
                    </temperature>
                    <alignment_procedure>
                        <basic />
                    </alignment_procedure>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>TVIPS TEMCAM-F416 (4k x 4k)</film_or_detector_model>
                            <digitization_details>
                                <dimensions>
                                    <width units="pixel">4096</width>
                                    <height units="pixel">4096</height>
                                </dimensions>
                                <sampling_interval units="&#181;m">15.6</sampling_interval>
                            </digitization_details>
                            <number_grids_imaged>1</number_grids_imaged>
                            <number_real_images>1159</number_real_images>
                            <average_exposure_time units="s">0.479</average_exposure_time>
                            <average_electron_dose_per_image units="e/&#8491;^2">30.0</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <image_recording_id>1</image_recording_id>
                <details>Automated image acquisition software Leginon was used for data collection.</details>
                <particle_selection>
                    <number_selected>221700</number_selected>
                    <details>Difference of Gaussian (DoG)-based automated particle picker, implemented in Appion processing package was used for particle selection.</details>
                </particle_selection>
                <ctf_correction>
                    <software_list>
                        <software>
                            <name>CTFFIND4</name>
                        </software>
                    </software_list>
                    <details>Ctffind4 was used for determining the CTF of each micrograph. Phases of each micrographs were flipped before particle extraction.</details>
                </ctf_correction>
                <startup_model type_of_model="OTHER">
                    <details>An initial 3D reference was generated with selected 2D class averages using sxviper program of the SPARX EM data processing package (sparx-em.org)</details>
                </startup_model>
                <final_reconstruction>
                    <number_classes_used>1</number_classes_used>
                    <applied_symmetry>
                        <point_group>C1</point_group>
                    </applied_symmetry>
                    <algorithm>FOURIER SPACE</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">15.6</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>1.4</version>
                        </software>
                    </software_list>
                    <number_images_used>26403</number_images_used>
                </final_reconstruction>
                <initial_angle_assignment>
                    <type>PROJECTION MATCHING</type>
                    <projection_matching_processing />
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>1.4</version>
                        </software>
                    </software_list>
                </initial_angle_assignment>
                <final_angle_assignment>
                    <type>PROJECTION MATCHING</type>
                    <projection_matching_processing />
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>1.4</version>
                        </software>
                    </software_list>
                </final_angle_assignment>
                <final_three_d_classification>
                    <number_classes>8</number_classes>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>1.4</version>
                        </software>
                    </software_list>
                </final_three_d_classification>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="3539">
        <file>emd_8558.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>96</col>
            <row>96</row>
            <sec>96</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>96</x>
            <y>96</y>
            <z>96</z>
        </spacing>
        <cell>
            <a units="&#8491;">393.59998</a>
            <b units="&#8491;">393.59998</b>
            <c units="&#8491;">393.59998</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>-0.09443157</minimum>
            <maximum>0.18779674</maximum>
            <average>0.0006248977</average>
            <std>0.010670355</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">4.1</x>
            <y units="&#8491;">4.1</y>
            <z units="&#8491;">4.1</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.0466</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-8558::::</label>
        <annotation_details>Negative stain reconstruction of Pseudomonas aeruginosa (PA14) Cas1-Cas2/3 complex</annotation_details>
    </map>
</emd>