<emd emdb_id="EMD-5590" version="3.0.1.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="https://github.com/emdb-empiar/emdb-schemas/blob/master/v3/v3_0_1_1/emdb_relaxed.xsd">
    <admin>
        <current_status>
            <code>REL</code>
            <processing_site>RCSB</processing_site>
        </current_status>
        <sites>
            <deposition>RCSB</deposition>
            <last_processing>RCSB</last_processing>
        </sites>
        <key_dates>
            <deposition>2013-02-27</deposition>
            <header_release>2013-04-03</header_release>
            <map_release>2013-04-03</map_release>
            <update>2013-11-06</update>
        </key_dates>
        <title>Electron cryo-microscopy of a cross-beta amyloid fibril polymorph</title>
        <authors_list>
            <author>Fitzpatrick AWP</author>
            <author>Debelouchina GT</author>
            <author>Bayro MJ</author>
            <author>Clare DK</author>
            <author>Caporini MA</author>
            <author>Bajaj VS</author>
            <author>Jaroniec CP</author>
            <author>Wang L</author>
            <author>Ladizhansky V</author>
            <author>Muller S</author>
            <author>MacPhee CE</author>
            <author>Waudby CA</author>
            <author>Mott HR</author>
            <author>De-Simone A</author>
            <author>Knowles TPJ</author>
            <author>Saibil HR</author>
            <author>Vendruscolo M</author>
            <author>Orlova EV</author>
            <author>Griffin RG</author>
            <author>Dobson CM</author>
        </authors_list>
        <keywords>amyloid fibrils, cross-beta structure, protein aggregation, polymorphism</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Fitzpatrick AW</author>
                    <author order="2">Debelouchina GT</author>
                    <author order="3">Bayro MJ</author>
                    <author order="4">Clare DK</author>
                    <author order="5">Caporini MA</author>
                    <author order="6">Bajaj VS</author>
                    <author order="7">Jaroniec CP</author>
                    <author order="8">Wang L</author>
                    <author order="9">Ladizhansky V</author>
                    <author order="10">Mueller SA</author>
                    <author order="11">Macphee CE</author>
                    <author order="12">Waudby CA</author>
                    <author order="13">Mott HR</author>
                    <author order="14">De Simone A</author>
                    <author order="15">Knowles TP</author>
                    <author order="16">Saibil HR</author>
                    <author order="17">Vendruscolo M</author>
                    <author order="18">Orlova EV</author>
                    <author order="19">Griffin RG</author>
                    <author order="20">Dobson CM</author>
                    <title>Atomic structure and hierarchical assembly of a cross-beta amyloid fibril.</title>
                    <journal>PROC.NAT.ACAD.SCI.USA</journal>
                    <volume>110</volume>
                    <first_page>5468</first_page>
                    <last_page>5473</last_page>
                    <year>2013</year>
                    <external_references type="PUBMED">23513222</external_references>
                    <external_references type="DOI">doi:10.1073/pnas.1219476110</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>2m5k</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>Doublet cross-beta amyloid fibril polymorph</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Doublet cross-beta amyloid fibril polymorph</name>
                <number_unique_components>1</number_unique_components>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>Transthyretin(105-115)</name>
                <natural_source database="NCBI">
                    <organism ncbi="10116">Rattus norvegicus</organism>
                    <synonym_organism>rat</synonym_organism>
                </natural_source>
                <recombinant_exp_flag>false</recombinant_exp_flag>
                <recombinant_expression database="NCBI" />
                <sequence />
            </protein_or_peptide>
        </macromolecule_list>
    </sample>
    <structure_determination_list>
        <structure_determination structure_determination_id="1">
            <method>singleParticle</method>
            <aggregation_state>filament</aggregation_state>
            <specimen_preparation_list>
                <single_particle_preparation preparation_id="1">
                    <concentration units="mg/mL">1</concentration>
                    <buffer>
                        <ph>2.0</ph>
                        <details>10% acetonitrile/water solution</details>
                    </buffer>
                    <grid>
                        <details>holey carbon films (R2/2, QuantifoilMicro Tools GmbH, Jena, Germany)</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">95</chamber_humidity>
                        <chamber_temperature units="K">99</chamber_temperature>
                        <instrument>HOMEMADE PLUNGER</instrument>
                        <method>Fibrils were applied to holey carbon films that were immediately plunge-frozen at liquid nitrogen temperature.</method>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>FEI TECNAI F20</microscope>
                    <illumination_mode>FLOOD BEAM</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>FIELD EMISSION GUN</electron_source>
                    <acceleration_voltage units="kV">200</acceleration_voltage>
                    <nominal_defocus_min units="&#181;m">0.9</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">3.0</nominal_defocus_max>
                    <nominal_magnification>40000.0</nominal_magnification>
                    <calibrated_magnification>40000.0</calibrated_magnification>
                    <specimen_holder_model>GATAN LIQUID NITROGEN</specimen_holder_model>
                    <temperature>
                        <temperature_min units="K">99</temperature_min>
                        <temperature_max units="K">100</temperature_max>
                        <temperature_average units="K">99</temperature_average>
                    </temperature>
                    <alignment_procedure>
                        <legacy>
                            <astigmatism>Objective lens astigmatism was corrected at 100,000 times magnification.</astigmatism>
                        </legacy>
                    </alignment_procedure>
                    <date>2006-03-03</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="FILM">KODAK SO-163 FILM</film_or_detector_model>
                            <digitization_details>
                                <scanner>ZEISS SCAI</scanner>
                            </digitization_details>
                            <number_real_images>250</number_real_images>
                        </image_recording>
                    </image_recording_list>
                    <specimen_holder>Nitrogen cooled</specimen_holder>
                    <tilt_angle_min>0</tilt_angle_min>
                    <tilt_angle_max>0</tilt_angle_max>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <details>The particles were selected using an automatic selection program.</details>
                <ctf_correction>
                    <details>CTFFIND3</details>
                </ctf_correction>
                <final_reconstruction>
                    <applied_symmetry>
                        <helical_parameters>
                            <delta_z units="&#8491;">4.67</delta_z>
                            <delta_phi units="deg">0.85</delta_phi>
                        </helical_parameters>
                    </applied_symmetry>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">12.7</resolution>
                    <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>SPIDER, IMAGIC, BKRP</name>
                        </software>
                    </software_list>
                    <number_images_used>82</number_images_used>
                </final_reconstruction>
                <final_two_d_classification>
                    <number_classes>18</number_classes>
                </final_two_d_classification>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
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        <file>emd_5590.map.gz</file>
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        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
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            <col>120</col>
            <row>120</row>
            <sec>298</sec>
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            <row>-59</row>
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            <a units="&#8491;">216.0</a>
            <b units="&#8491;">216.0</b>
            <c units="&#8491;">536.39996</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>-129.46867370999999</minimum>
            <maximum>860.173217769999951</maximum>
            <average>19.60117722</average>
            <std>97.20013428</std>
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        <pixel_spacing>
            <x units="&#8491;">1.8</x>
            <y units="&#8491;">1.8</y>
            <z units="&#8491;">1.7999998</z>
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        <contour_list>
            <contour primary="true">
                <level>230.430000000000007</level>
                <source>AUTHOR</source>
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        </contour_list>
        <annotation_details>Reconstruction of doublet cross-beta amyloid fibril polymorph</annotation_details>
        <details>::::EMDATABANK.org::::EMD-5590::::</details>
    </map>
</emd>