<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" emdb_id="EMD-8999" version="3.0.0.1" xsi:schemaLocation="https://github.com/emdb-empiar/emdb-schemas/blob/master/v3/v3_0_0_1/emdb.xsd">
    <admin>
        <current_status>
            <date>2018-10-10</date>
            <code>REL</code>
            <processing_site>RCSB</processing_site>
        </current_status>
        <sites>
            <deposition>RCSB</deposition>
            <last_processing>RCSB</last_processing>
        </sites>
        <key_dates>
            <deposition>2018-07-26</deposition>
            <header_release>2018-08-08</header_release>
            <map_release>2018-08-22</map_release>
            <update>2018-10-10</update>
        </key_dates>
        <title>Beam-tilt dependency of single-particle cryo-EM map quality: Expt 2 at 0 mrad</title>
        <authors_list>
            <author>Cheng A</author>
            <author>Eng ET</author>
            <author>Alink L</author>
            <author>Rice WJ</author>
            <author>Jordan KD</author>
            <author>Kim LY</author>
            <author>Potter CS</author>
            <author>Carragher B</author>
        </authors_list>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Cheng A</author>
                    <author order="2">Eng ET</author>
                    <author order="3">Alink L</author>
                    <author order="4">Rice WJ</author>
                    <author order="5">Jordan KD</author>
                    <author order="6">Kim LY</author>
                    <author order="7">Potter CS</author>
                    <author order="8">Carragher B</author>
                    <title>High resolution single particle cryo-electron microscopy using beam-image shift.</title>
                    <journal_abbreviation>J. Struct. Biol.</journal_abbreviation>
                    <country>US</country>
                    <volume>204</volume>
                    <first_page>270</first_page>
                    <last_page>275</last_page>
                    <year>2018</year>
                    <external_references type="PUBMED">30055234</external_references>
                    <external_references type="DOI">doi:10.1016/j.jsb.2018.07.015</external_references>
                    <external_references type="ISSN">1095-8657</external_references>
                    <external_references type="CSD">0803</external_references>
                    <external_references type="ASTM">JSBIEM</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-8999</emdb_id>
                <relationship>
                    <other>associated EM volume</other>
                </relationship>
            </emdb_reference>
        </emdb_list>
    </crossreferences>
    <sample>
        <name>Thermoplasma acidophilum 20S proteasome</name>
        <supramolecule_list>
            <complex_supramolecule supramolecule_id="1">
                <name>Thermoplasma acidophilum 20S proteasome</name>
                <parent>0</parent>
                <natural_source database="NCBI">
                    <organism ncbi="2303">Thermoplasma acidophilum</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.7</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">0.9</concentration>
                    <buffer>
                        <ph>8.</ph>
                        <component>
                            <concentration units="mM">20.0</concentration>
                            <name>Tris</name>
                        </component>
                        <component>
                            <concentration units="mM">150.0</concentration>
                            <formula>NaCl</formula>
                        </component>
                    </buffer>
                    <grid>
                        <model>C-flat-1.2/1.3</model>
                        <material>COPPER</material>
                        <mesh>400</mesh>
                        <support_film film_type_id="1">
                            <film_material>CARBON</film_material>
                            <film_topology>HOLEY</film_topology>
                        </support_film>
                        <pretreatment>
                            <type>PLASMA CLEANING</type>
                            <atmosphere>OTHER</atmosphere>
                        </pretreatment>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">75</chamber_humidity>
                        <chamber_temperature units="K">298</chamber_temperature>
                        <instrument>GATAN CRYOPLUNGE 3</instrument>
                        <details>blotted for 2.5 s after 30 s wait time. </details>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>FEI TITAN KRIOS</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>
                    <c2_aperture_diameter units="&#181;m">70.0</c2_aperture_diameter>
                    <nominal_cs units="mm">2.7</nominal_cs>
                    <nominal_defocus_min units="&#181;m">0.8</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">2.0</nominal_defocus_max>
                    <nominal_magnification>130000.</nominal_magnification>
                    <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
                    <cooling_holder_cryogen>NITROGEN</cooling_holder_cryogen>
                    <alignment_procedure>
                        <other />
                    </alignment_procedure>
                    <specialist_optics>
                        <energy_filter>
                            <name>GIF Quantum LS</name>
                            <slit_width units="eV">15</slit_width>
                        </energy_filter>
                    </specialist_optics>
                    <details>0,0 beam-image shift with Intentionally beam-shift pivot misalignment.</details>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>GATAN K2 SUMMIT (4k x 4k)</film_or_detector_model>
                            <detector_mode>COUNTING</detector_mode>
                            <digitization_details>
                                <dimensions>
                                    <width units="pixel">3710</width>
                                    <height units="pixel">3838</height>
                                </dimensions>
                                <sampling_interval units="&#181;m">5.0</sampling_interval>
                                <frames_per_image>2-60</frames_per_image>
                            </digitization_details>
                            <number_grids_imaged>1</number_grids_imaged>
                            <number_real_images>545</number_real_images>
                            <average_exposure_time units="s">6.0</average_exposure_time>
                            <average_electron_dose_per_image units="e/&#8491;^2">0.71</average_electron_dose_per_image>
                            <details>of the 545 images, 158 images were removed from processing because of empty or high drift movie.</details>
                        </image_recording>
                    </image_recording_list>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <image_recording_id>1</image_recording_id>
                <ctf_correction>
                    <software_list>
                        <software>
                            <name>CTFFIND</name>
                            <version>4</version>
                        </software>
                    </software_list>
                </ctf_correction>
                <startup_model type_of_model="NONE">
                    <details>CryoSPARC ab initio</details>
                </startup_model>
                <final_reconstruction>
                    <number_classes_used>1</number_classes_used>
                    <applied_symmetry>
                        <point_group>D7</point_group>
                    </applied_symmetry>
                    <algorithm>BACK PROJECTION</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">2.74</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>cryoSPARC</name>
                            <version>0.6.5</version>
                        </software>
                    </software_list>
                    <number_images_used>11400</number_images_used>
                </final_reconstruction>
                <initial_angle_assignment>
                    <type>MAXIMUM LIKELIHOOD</type>
                    <software_list>
                        <software>
                            <name>cryoSPARC</name>
                            <version>0.6.5</version>
                        </software>
                    </software_list>
                </initial_angle_assignment>
                <final_angle_assignment>
                    <type>MAXIMUM LIKELIHOOD</type>
                </final_angle_assignment>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="67109">
        <file>emd_8999.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>256</col>
            <row>256</row>
            <sec>256</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>256</x>
            <y>256</y>
            <z>256</z>
        </spacing>
        <cell>
            <a units="&#8491;">271.488</a>
            <b units="&#8491;">271.488</b>
            <c units="&#8491;">271.488</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>-4.1709642</minimum>
            <maximum>6.7849107</maximum>
            <average>0.0019432057</average>
            <std>0.31377828</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">1.0605</x>
            <y units="&#8491;">1.0605</y>
            <z units="&#8491;">1.0605</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>1.05</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-8999::::</label>
        <annotation_details>Sharpened 0 beam tilt map in Experiment 2</annotation_details>
    </map>
</emd>