<?xml version="1.0" encoding="UTF-8"?>
<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="https://github.com/emdb-empiar/emdb-schemas/blob/master/v3/v3_0_1_5/emdb.xsd" emdb_id="EMD-0529" version="3.0.1.6">
    <admin>
        <current_status>
            <date>2019-11-27</date>
            <code>REL</code>
            <processing_site>RCSB</processing_site>
        </current_status>
        <sites>
            <deposition>RCSB</deposition>
            <last_processing>RCSB</last_processing>
        </sites>
        <key_dates>
            <deposition>2019-02-07</deposition>
            <header_release>2019-10-30</header_release>
            <map_release>2019-10-30</map_release>
            <update>2019-11-27</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>National Institutes of Health/National Institute of General Medical Sciences</funding_body>
                <code>GM080139</code>
                <country>United States</country>
            </grant_reference>
        </grant_support>
        <title>Purified ribosome - A complete data processing workflow for CryoET and subtomogram averaging</title>
        <authors_list>
            <author>Chen M</author>
            <author>Bell JM</author>
            <author>Ludtke SJ</author>
        </authors_list>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Chen M</author>
                    <author order="2">Bell JM</author>
                    <author order="3">Shi X</author>
                    <author order="4">Sun SY</author>
                    <author order="5">Wang Z</author>
                    <author order="6">Ludtke SJ</author>
                    <title>A complete data processing workflow for cryo-ET and subtomogram averaging.</title>
                    <journal_abbreviation>Nat.Methods</journal_abbreviation>
                    <country>US</country>
                    <volume>16</volume>
                    <first_page>1161</first_page>
                    <last_page>1168</last_page>
                    <year>2019</year>
                    <external_references type="PUBMED">31611690</external_references>
                    <external_references type="DOI">doi:10.1038/s41592-019-0591-8</external_references>
                    <external_references type="ISSN">1548-7105</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-3420</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
                <details>Structure from the same dataset</details>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-0529</emdb_id>
                <relationship>
                    <other>associated EM volume</other>
                </relationship>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-0530</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
            </emdb_reference>
        </emdb_list>
    </crossreferences>
    <sample>
        <name>Ribosome from EMPIAR-10064, MixedCTEM dataset</name>
        <supramolecule_list>
            <complex_supramolecule supramolecule_id="1">
                <name>Ribosome from EMPIAR-10064, MixedCTEM dataset</name>
                <parent>0</parent>
                <natural_source database="NCBI">
                    <organism ncbi="9986">Oryctolagus cuniculus</organism>
                </natural_source>
            </complex_supramolecule>
        </supramolecule_list>
    </sample>
    <structure_determination_list>
        <structure_determination structure_determination_id="1">
            <method>tomography</method>
            <aggregation_state>particle</aggregation_state>
            <specimen_preparation_list>
                <tomography_preparation preparation_id="1">
                    <buffer>
                        <ph>7</ph>
                    </buffer>
                    <grid>
                        <details>unspecified</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <details></details>
                    </vitrification>
                    <sectioning>
                        <other_sectioning>NO SECTIONING</other_sectioning>
                    </sectioning>
                </tomography_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <tomography_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>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>GATAN K2 SUMMIT (4k x 4k)</film_or_detector_model>
                            <average_electron_dose_per_image units="e/Å^2">30.0</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                </tomography_microscopy>
            </microscopy_list>
            <tomography_processing image_processing_id="1">
                <image_recording_id>1</image_recording_id>
                <final_reconstruction>
                    <algorithm>FOURIER SPACE</algorithm>
                    <resolution units="Å" res_type="BY AUTHOR">8.4</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>EMAN2</name>
                            <version>2.3</version>
                        </software>
                    </software_list>
                    <number_images_used>3239</number_images_used>
                </final_reconstruction>
                <ctf_correction>
                    <software_list>
                        <software>
                            <name>EMAN2</name>
                            <version>2.3</version>
                        </software>
                    </software_list>
                </ctf_correction>
            </tomography_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="23329">
        <file>emd_0529.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>180</col>
            <row>180</row>
            <sec>180</sec>
        </dimensions>
        <origin>
            <col>-90</col>
            <row>-90</row>
            <sec>-90</sec>
        </origin>
        <spacing>
            <x>180</x>
            <y>180</y>
            <z>180</z>
        </spacing>
        <cell>
            <a units="Å">471.59998</a>
            <b units="Å">471.59998</b>
            <c units="Å">471.59998</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>-2.7292383</minimum>
            <maximum>6.8252907</maximum>
            <average>0.062119965</average>
            <std>0.4563232</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">2.62</x>
            <y units="Å">2.62</y>
            <z units="Å">2.62</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::D_1000239607::::</label>
        <annotation_details>Averaged structure of purified ribosome from EMPIAR-10064 dataset, after subtilt refinement in EMAN2.</annotation_details>
    </map>
    <interpretation>
        <additional_map_list>
            <additional_map format="CCP4" size_kbytes="23329">
                <file>emd_0529_additional.map.gz</file>
                <symmetry>
                    <space_group>1</space_group>
                </symmetry>
                <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
                <dimensions>
                    <col>180</col>
                    <row>180</row>
                    <sec>180</sec>
                </dimensions>
                <origin>
                    <col>-90</col>
                    <row>-90</row>
                    <sec>-90</sec>
                </origin>
                <spacing>
                    <x>180</x>
                    <y>180</y>
                    <z>180</z>
                </spacing>
                <cell>
                    <a units="Å">471.59998</a>
                    <b units="Å">471.59998</b>
                    <c units="Å">471.59998</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>-3.5450583</minimum>
                    <maximum>10.700572</maximum>
                    <average>0.21827725</average>
                    <std>0.9519271</std>
                </statistics>
                <pixel_spacing>
                    <x units="Å">2.62</x>
                    <y units="Å">2.62</y>
                    <z units="Å">2.62</z>
                </pixel_spacing>
                <contour_list>
                    <contour primary="true">
                        <source>AUTHOR</source>
                    </contour>
                </contour_list>
                <label>::::EMDATABANK.org::::D_1000239607::::</label>
                <annotation_details>Averaged structure after subtomogram refinement but before subtilt refinement</annotation_details>
            </additional_map>
        </additional_map_list>
    </interpretation>
</emd>
