<?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_8/emdb.xsd" emdb_id="EMD-9859" version="3.0.1.8">
    <admin>
        <current_status>
            <date>2020-03-25</date>
            <code>REL</code>
            <processing_site>PDBj</processing_site>
        </current_status>
        <sites>
            <deposition>PDBj</deposition>
            <last_processing>PDBj</last_processing>
        </sites>
        <key_dates>
            <deposition>2019-03-20</deposition>
            <header_release>2020-03-25</header_release>
            <map_release>2020-03-25</map_release>
            <update>2020-03-25</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>Japan Society for the Promotion of Science</funding_body>
                <code>JP26119002</code>
                <country>Japan</country>
            </grant_reference>
        </grant_support>
        <title>Structure of the archaeal Archaeoglobus fulgidus oligosaccharyltransferase (AfAglB-L) trapped in amphipol</title>
        <authors_list>
            <author>Kawasaki Y</author>
            <author>Mayanagi K</author>
            <author>Kohda D</author>
        </authors_list>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="false">
                    <author order="1">Kawasaki Y</author>
                    <author order="2">Mayanagi K</author>
                    <author order="3">Kohda D</author>
                    <title>Structure of the archaeal Archaeoglobus fulgidus oligosaccharyltransferase (AfAglB-L) trapped in amphipol</title>
                    <journal_abbreviation>To Be Published</journal_abbreviation>
                    <external_references type="CSD">0353</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-9859</emdb_id>
                <relationship>
                    <other>associated EM volume</other>
                </relationship>
            </emdb_reference>
        </emdb_list>
    </crossreferences>
    <sample>
        <name>Archaeoglobus fulgidus oligosaccharyltransferase (AfAglB-L) trapped in amphipol</name>
        <supramolecule_list>
            <complex_supramolecule supramolecule_id="1">
                <name>Archaeoglobus fulgidus oligosaccharyltransferase (AfAglB-L) trapped in amphipol</name>
                <parent>0</parent>
                <natural_source database="NCBI">
                    <organism ncbi="2234">Archaeoglobus fulgidus</organism>
                </natural_source>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                </recombinant_expression>
            </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">
                    <buffer>
                        <ph>7.4</ph>
                        <component>
                            <concentration units="mM">20.0</concentration>
                            <formula>C4H11NO3</formula>
                            <name>Tris-HCl</name>
                        </component>
                        <component>
                            <concentration units="mM">100.0</concentration>
                            <formula>NaCl</formula>
                            <name>sodium chloride</name>
                        </component>
                        <details>20 mM Tris-HCl (pH 7.4), 100 mM NaCl</details>
                    </buffer>
                    <staining>
                        <type>NEGATIVE</type>
                        <material>uranyl acetate</material>
                        <details>Negatively stained EM specimens were prepared using uranyl-acetate stain.</details>
                    </staining>
                    <grid>
                        <model>Homemade</model>
                        <material>COPPER</material>
                        <mesh>200</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>
                        </pretreatment>
                    </grid>
                    <details>The sample was monodisperse</details>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>FEI TECNAI 20</microscope>
                    <illumination_mode>FLOOD BEAM</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>LAB6</electron_source>
                    <acceleration_voltage units="kV">200</acceleration_voltage>
                    <nominal_cs units="mm">2.0</nominal_cs>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>FEI EAGLE (2k x 2k)</film_or_detector_model>
                            <digitization_details>
                                <dimensions>
                                    <width units="pixel">2048</width>
                                    <height units="pixel">2048</height>
                                </dimensions>
                            </digitization_details>
                            <number_grids_imaged>1</number_grids_imaged>
                            <number_real_images>170</number_real_images>
                            <average_exposure_time units="s">120.0</average_exposure_time>
                            <average_electron_dose_per_image units="e/Å^2">50.0</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>
                <particle_selection>
                    <number_selected>11122</number_selected>
                </particle_selection>
                <final_reconstruction>
                    <applied_symmetry>
                        <point_group>C1</point_group>
                    </applied_symmetry>
                    <algorithm>BACK PROJECTION</algorithm>
                    <resolution units="Å" res_type="BY AUTHOR">21.0</resolution>
                    <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>EMAN</name>
                            <version>1.9</version>
                            <processing_details>EMAN refine command was used.</processing_details>
                        </software>
                    </software_list>
                    <number_images_used>11122</number_images_used>
                </final_reconstruction>
                <initial_angle_assignment>
                    <type>COMMON LINE</type>
                    <software_list>
                        <software>
                            <name>EMAN</name>
                            <version>1.9</version>
                            <processing_details>EMAN StartAny command was used.</processing_details>
                        </software>
                    </software_list>
                </initial_angle_assignment>
                <final_angle_assignment>
                    <type>PROJECTION MATCHING</type>
                    <projection_matching_processing>
                        <number_reference_projections>180</number_reference_projections>
                    </projection_matching_processing>
                    <software_list>
                        <software>
                            <name>EMAN</name>
                            <version>1.9</version>
                            <processing_details>EMAN refine command was used.</processing_details>
                        </software>
                    </software_list>
                </final_angle_assignment>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="2049">
        <file>emd_9859.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>80</col>
            <row>80</row>
            <sec>80</sec>
        </dimensions>
        <origin>
            <col>-14</col>
            <row>-14</row>
            <sec>-14</sec>
        </origin>
        <spacing>
            <x>80</x>
            <y>80</y>
            <z>80</z>
        </spacing>
        <cell>
            <a units="Å">220.8</a>
            <b units="Å">220.8</b>
            <c units="Å">220.8</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>-3.7689376</minimum>
            <maximum>9.383638</maximum>
            <average>-0.00000000130</average>
            <std>1.0000001</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">2.76</x>
            <y units="Å">2.76</y>
            <z units="Å">2.76</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>2.66</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-9859::::</label>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <initial_model>
                    <access_code>3WAK</access_code>
                    <chain>
                        <chain_id>A</chain_id>
                        <residue_range>5-868</residue_range>
                    </chain>
                </initial_model>
                <refinement_protocol>RIGID BODY FIT</refinement_protocol>
                <details>Fitting was done using Chimera.</details>
                <refinement_space>REAL</refinement_space>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>
