<?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_7/emdb.xsd" emdb_id="EMD-0019" version="3.0.1.7">
    <admin>
        <current_status>
            <date>2020-01-15</date>
            <code>REL</code>
            <processing_site>PDBe</processing_site>
        </current_status>
        <sites>
            <deposition>PDBe</deposition>
            <last_processing>PDBe</last_processing>
        </sites>
        <key_dates>
            <deposition>2018-05-18</deposition>
            <header_release>2018-06-20</header_release>
            <map_release>2019-06-19</map_release>
            <update>2020-01-15</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>European Research Council</funding_body>
                <code>322408</code>
                <country>United Kingdom</country>
            </grant_reference>
            <grant_reference>
                <funding_body>National Institutes of Health/National Institute of General Medical Sciences</funding_body>
                <code>AG-058504</code>
                <country>United States</country>
            </grant_reference>
            <grant_reference>
                <funding_body>National Institutes of Health/National Institute of General Medical Sciences</funding_body>
                <code>EB-002026</code>
                <country>United States</country>
            </grant_reference>
            <grant_reference>
                <funding_body>Wellcome Trust</funding_body>
                <code>204963</code>
                <country>United Kingdom</country>
            </grant_reference>
            <grant_reference>
                <funding_body>Wellcome Trust</funding_body>
                <code>092896MA</code>
                <country>United Kingdom</country>
            </grant_reference>
        </grant_support>
        <title>Four protofilament beta-2-microglobulin amyloid fibril</title>
        <authors_list>
            <author>Iadanza MG</author>
            <author>Ranson NA</author>
        </authors_list>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Iadanza MG</author>
                    <author order="2">Ranson NA</author>
                    <title>n/a</title>
                    <journal_abbreviation>Not Published</journal_abbreviation>
                    <external_references type="CSD">0353</external_references>
                </journal_citation>
            </primary_citation>
            <secondary_citation>
                <journal_citation published="true">
                    <author order="3">Iadanza MG</author>
                    <author order="4">Silvers R</author>
                    <author order="5">Boardman J</author>
                    <author order="6">Smith HI</author>
                    <author order="7">Karamanon TK</author>
                    <author order="8">Debelouchina GT</author>
                    <author order="9">Su Y</author>
                    <author order="10">Griffin RG</author>
                    <author order="11">Ranson NA</author>
                    <author order="12">Radford SE</author>
                    <title>The structure of a Beta 2-microglobulin fibril suggests a molecular basis for its amyloid polymorphism</title>
                    <journal_abbreviation>Nat Commun.</journal_abbreviation>
                    <country>UK</country>
                    <year>2018</year>
                    <external_references type="PUBMED">30375379</external_references>
                    <external_references type="DOI">doi:10.1038/s41467-018-06761-6</external_references>
                    <external_references type="ISSN">2041-1723</external_references>
                </journal_citation>
            </secondary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-0019</emdb_id>
                <relationship>
                    <other>associated EM volume</other>
                </relationship>
                <details>Two protofilament beta-2-microglobulin amyloid fibril</details>
            </emdb_reference>
        </emdb_list>
    </crossreferences>
    <sample>
        <name>four protofilament beta-2-microglobulin amyloid fibril</name>
        <supramolecule_list>
            <complex_supramolecule supramolecule_id="1">
                <name>four protofilament beta-2-microglobulin amyloid fibril</name>
                <parent>0</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>1</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                </natural_source>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                </recombinant_expression>
                <molecular_weight>
                    <theoretical units="MDa">0.0117</theoretical>
                </molecular_weight>
            </complex_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>Human beta-2-microglobulin</name>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                </natural_source>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDW
SFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM</string>
                </sequence>
            </protein_or_peptide>
        </macromolecule_list>
    </sample>
    <structure_determination_list>
        <structure_determination structure_determination_id="1">
            <method>helical</method>
            <aggregation_state>filament</aggregation_state>
            <specimen_preparation_list>
                <helical_preparation preparation_id="1">
                    <concentration units="mg/mL">0.025</concentration>
                    <buffer>
                        <ph>2.5</ph>
                        <component>
                            <concentration units="mM">20.0</concentration>
                            <formula>CH3COONa</formula>
                            <name>Sodium Acetate</name>
                        </component>
                        <component>
                            <concentration units="mM">20.0</concentration>
                            <formula>Na3PO4</formula>
                            <name>Sodium phosphate</name>
                        </component>
                        <component>
                            <concentration units="%">0.01</concentration>
                            <formula>NaN3</formula>
                            <name>Sodium Azide</name>
                        </component>
                    </buffer>
                    <grid>
                        <model>Quantifoil R3.5/1</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>
                        </pretreatment>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">80</chamber_humidity>
                        <chamber_temperature units="K">281.15</chamber_temperature>
                        <instrument>FEI VITROBOT MARK II</instrument>
                        <details></details>
                    </vitrification>
                    <details>Quiescent growth at 0.25 mg/ml for 5 weeks, diluted 10x with buffer</details>
                </helical_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <helical_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">100.0</c2_aperture_diameter>
                    <nominal_cs units="mm">2.7</nominal_cs>
                    <nominal_defocus_min units="µm">0.00175</nominal_defocus_min>
                    <nominal_defocus_max units="µm">0.00325</nominal_defocus_max>
                    <nominal_magnification>130000.0</nominal_magnification>
                    <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>
                            <digitization_details>
                                <frames_per_image>3-40</frames_per_image>
                            </digitization_details>
                            <number_grids_imaged>1</number_grids_imaged>
                            <number_real_images>5549</number_real_images>
                            <average_exposure_time units="s">10.0</average_exposure_time>
                            <average_electron_dose_per_image units="e/Å^2">38.5</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                </helical_microscopy>
            </microscopy_list>
            <helical_processing image_processing_id="1">
                <image_recording_id>1</image_recording_id>
                <final_reconstruction>
                    <number_classes_used>1</number_classes_used>
                    <applied_symmetry>
                        <helical_parameters>
                            <delta_z units="Å">2.3</delta_z>
                            <delta_phi units="deg">-0.161</delta_phi>
                            <axial_symmetry>C1</axial_symmetry>
                        </helical_parameters>
                    </applied_symmetry>
                    <algorithm>FOURIER SPACE</algorithm>
                    <resolution units="Å" res_type="BY AUTHOR">9.42</resolution>
                    <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>RELION</name>
                        </software>
                    </software_list>
                    <details>Resolution estimated using rmeasure software</details>
                    <number_images_used>8891</number_images_used>
                </final_reconstruction>
                <ctf_correction>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>2.1</version>
                        </software>
                        <software>
                            <name>Gctf</name>
                        </software>
                    </software_list>
                </ctf_correction>
                <startup_model type_of_model="OTHER">
                    <details>Double protofilament map from same study
Filtered to 60 Angstrom resolution</details>
                </startup_model>
                <final_angle_assignment>
                    <type>NOT APPLICABLE</type>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>2.1</version>
                        </software>
                    </software_list>
                </final_angle_assignment>
            </helical_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="864001">
        <file>emd_0019.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>600</col>
            <row>600</row>
            <sec>600</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>600</x>
            <y>600</y>
            <z>600</z>
        </spacing>
        <cell>
            <a units="Å">635.99994</a>
            <b units="Å">635.99994</b>
            <c units="Å">635.99994</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>-0.005038559</minimum>
            <maximum>0.019340014</maximum>
            <average>0.00028363764</average>
            <std>0.0018114602</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">1.06</x>
            <y units="Å">1.06</y>
            <z units="Å">1.06</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.0089</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-0019::::</label>
        <annotation_details>Four protofilament beta-2-microglobulin amyloid fibril</annotation_details>
    </map>
</emd>
