<?xml version="1.0" encoding="UTF-8"?>
<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="https://ftp.ebi.ac.uk/pub/databases/em_ebi/emdb_related/emdb-schemas/emdb_schemas/v3/v3_0_9_0/emdb.xsd" version="3.0.9.0" emdb_id="EMD-13881">
    <admin>
        <current_status>
            <date>2023-12-13</date>
            <code>REL</code>
            <processing_site>PDBe</processing_site>
        </current_status>
        <sites>
            <deposition>PDBe</deposition>
            <last_processing>PDBe</last_processing>
        </sites>
        <key_dates>
            <deposition>2021-11-16</deposition>
            <header_release>2022-01-26</header_release>
            <map_release>2022-01-26</map_release>
            <update>2023-12-13</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>Wellcome Trust</funding_body>
                <code>202231/Z/16/Z</code>
                <country>United Kingdom</country>
            </grant_reference>
        </grant_support>
        <title>CS-TV2-reconstructed tomogram of a C. crescentus stalk covered by an S-layer</title>
        <authors_list>
            <author ORCID="0000-0002-0168-0277">Bharat TAM</author>
            <author ORCID="0000-0002-6242-1041">Boehning J</author>
            <author ORCID="0000-0002-5151-6360">Collins SM</author>
        </authors_list>
        <keywords>S-layer, C. crescentus, RsaA, STRUCTURAL PROTEIN</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Bohning J</author>
                    <author order="2">Bharat TAM</author>
                    <author order="3">Collins SM</author>
                    <title>Compressed sensing for electron cryotomography and high-resolution subtomogram averaging of biological specimens.</title>
                    <journal_abbreviation>Structure</journal_abbreviation>
                    <country>UK</country>
                    <volume>30</volume>
                    <first_page>408</first_page>
                    <last_page>417.e4</last_page>
                    <year>2022</year>
                    <external_references type="PUBMED">35051366</external_references>
                    <external_references type="DOI">doi:10.1016/j.str.2021.12.010</external_references>
                    <external_references type="ISSN">0969-2126</external_references>
                    <external_references type="CSD">2005</external_references>
                    <external_references type="ASTM">STRUE6</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>C. crescentus stalk</name>
        <supramolecule_list>
            <organelle_or_cellular_component_supramolecule supramolecule_id="1">
                <name>C. crescentus stalk</name>
                <parent>0</parent>
                <details>C. crescentus stalk, covered by an S-layer of RsaA hexamers.</details>
                <natural_source database="NCBI">
                    <organism ncbi="155892">Caulobacter vibrioides</organism>
                    <strain>CB15</strain>
                    <cellular_location>Stalk</cellular_location>
                </natural_source>
            </organelle_or_cellular_component_supramolecule>
        </supramolecule_list>
    </sample>
    <structure_determination_list>
        <structure_determination structure_determination_id="1">
            <method>tomography</method>
            <aggregation_state>cell</aggregation_state>
            <specimen_preparation_list>
                <tomography_preparation preparation_id="1">
                    <buffer>
                        <ph>7.4</ph>
                    </buffer>
                    <grid>
                        <model>Quantifoil R3.5/1</model>
                        <material>COPPER/RHODIUM</material>
                        <mesh>200</mesh>
                        <support_film film_type_id="1">
                            <film_material>CARBON</film_material>
                            <film_topology>HOLEY ARRAY</film_topology>
                        </support_film>
                        <pretreatment>
                            <type>GLOW DISCHARGE</type>
                        </pretreatment>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">100</chamber_humidity>
                        <chamber_temperature units="K">283</chamber_temperature>
                        <instrument>FEI VITROBOT MARK IV</instrument>
                    </vitrification>
                    <details>Please see Bharat et al, Nature Microbiology 2017</details>
                    <fiducial_markers_list>
                        <fiducial_marker>
                            <manufacturer>CMC Utrecht</manufacturer>
                            <diameter units="nanometer">10</diameter>
                        </fiducial_marker>
                    </fiducial_markers_list>
                    <cryo_protectant>None</cryo_protectant>
                    <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>
                    <c2_aperture_diameter units="µm">50.0</c2_aperture_diameter>
                    <nominal_cs units="mm">2.7</nominal_cs>
                    <nominal_defocus_min units="µm">3.5</nominal_defocus_min>
                    <nominal_defocus_max units="µm">3.5</nominal_defocus_max>
                    <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
                    <cooling_holder_cryogen>NITROGEN</cooling_holder_cryogen>
                    <alignment_procedure>
                        <coma_free/>
                    </alignment_procedure>
                    <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>
                            <average_electron_dose_per_image units="e/Å^2">0.578</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>
                    <software_list>
                        <software>
                            <name>IMOD</name>
                        </software>
                    </software_list>
                    <details>CS-TV2 reconstruction algorithm as described in manuscript was used.</details>
                    <number_images_used>121</number_images_used>
                </final_reconstruction>
            </tomography_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="1023423">
        <file>emd_13881.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>3600</col>
            <row>1001</row>
            <sec>71</sec>
        </dimensions>
        <origin>
            <col>458</col>
            <row>578</row>
            <sec>-124</sec>
        </origin>
        <spacing>
            <x>3600</x>
            <y>1001</y>
            <z>71</z>
        </spacing>
        <cell>
            <a units="Å">16081.2</a>
            <b units="Å">4471.467</b>
            <c units="Å">317.157</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>0.0</minimum>
            <maximum>0.004115206</maximum>
            <average>0.000043299762</average>
            <std>0.00010632376</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">4.467</x>
            <y units="Å">4.467</y>
            <z units="Å">4.467</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-13881::::</label>
        <annotation_details>CS-TV2 reconstruction of a C. crescentus stalk covered by an S-layer of RsaA hexamers. The tomogram was cropped and rotated to reduce file size. Contrast may require manual adjustment.</annotation_details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <refinement_protocol>OTHER</refinement_protocol>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>
