<?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_8_0/emdb.xsd" version="3.0.8.0" emdb_id="EMD-20645">
    <admin>
        <current_status>
            <date>2023-10-11</date>
            <code>REL</code>
            <processing_site>RCSB</processing_site>
        </current_status>
        <sites>
            <deposition>RCSB</deposition>
            <last_processing>RCSB</last_processing>
        </sites>
        <key_dates>
            <deposition>2019-08-27</deposition>
            <header_release>2019-09-25</header_release>
            <map_release>2020-01-29</map_release>
            <update>2023-10-11</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)</funding_body>
                <code>GM123159</code>
                <country>United States</country>
            </grant_reference>
            <grant_reference>
                <funding_body>National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)</funding_body>
                <code>GM124149</code>
                <country>United States</country>
            </grant_reference>
            <grant_reference>
                <funding_body>National Science Foundation (NSF, United States)</funding_body>
                <code>STC-1231306</code>
                <country>United States</country>
            </grant_reference>
            <grant_reference>
                <funding_body>National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)</funding_body>
                <code>GM117126</code>
                <country>United States</country>
            </grant_reference>
        </grant_support>
        <title>MicroED structure of a FIB-milled CypA Crystal</title>
        <authors_list>
            <author>Wolff AM</author>
            <author>Martynowycz MW</author>
            <author>Zhao W</author>
            <author>Gonen T</author>
            <author>Fraser JS</author>
            <author>Thompson MC</author>
        </authors_list>
        <keywords>Peptidyl-prolyl, cis-trans, isomerase, cyclophilin</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author ORCID="0000-0003-0474-7673" order="1">Wolff AM</author>
                    <author ORCID="0000-0003-4713-9504" order="2">Young ID</author>
                    <author ORCID="0000-0002-6253-8282" order="3">Sierra RG</author>
                    <author ORCID="0000-0002-0908-7822" order="4">Brewster AS</author>
                    <author ORCID="0000-0003-0055-230X" order="5">Martynowycz MW</author>
                    <author ORCID="0000-0001-9851-7355" order="6">Nango E</author>
                    <author order="7">Sugahara M</author>
                    <author ORCID="0000-0003-2697-2767" order="8">Nakane T</author>
                    <author order="9">Ito K</author>
                    <author order="10">Aquila A</author>
                    <author order="11">Bhowmick A</author>
                    <author ORCID="0000-0002-0935-8362" order="12">Biel JT</author>
                    <author ORCID="0000-0002-5292-4470" order="13">Carbajo S</author>
                    <author ORCID="0000-0003-2414-9427" order="14">Cohen AE</author>
                    <author order="15">Cortez S</author>
                    <author order="16">Gonzalez A</author>
                    <author ORCID="0000-0002-8813-4622" order="17">Hino T</author>
                    <author order="18">Im D</author>
                    <author ORCID="0000-0001-8289-0497" order="19">Koralek JD</author>
                    <author ORCID="0000-0001-8691-6252" order="20">Kubo M</author>
                    <author order="21">Lazarou TS</author>
                    <author order="22">Nomura T</author>
                    <author order="23">Owada S</author>
                    <author order="24">Samelson A</author>
                    <author order="25">Tanaka T</author>
                    <author order="26">Tanaka R</author>
                    <author order="27">Thompson EM</author>
                    <author ORCID="0000-0003-2358-841X" order="28">van den Bedem H</author>
                    <author ORCID="0000-0003-0737-8383" order="29">Woldeyes RA</author>
                    <author ORCID="0000-0002-9592-397X" order="30">Yumoto F</author>
                    <author order="31">Zhao W</author>
                    <author order="32">Tono K</author>
                    <author order="33">Boutet S</author>
                    <author order="34">Iwata S</author>
                    <author ORCID="0000-0002-9254-4069" order="35">Gonen T</author>
                    <author order="36">Sauter NK</author>
                    <author ORCID="0000-0002-5080-2859" order="37">Fraser JS</author>
                    <author ORCID="0000-0002-6099-2027" order="38">Thompson MC</author>
                    <title>Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals</title>
                    <journal_abbreviation>Iucrj</journal_abbreviation>
                    <country>UK</country>
                    <volume>7</volume>
                    <first_page>306</first_page>
                    <last_page>323</last_page>
                    <year>2020</year>
                    <external_references type="DOI">doi:10.1107/S205225252000072X</external_references>
                    <external_references type="ISSN">2052-2525</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>6u5g</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>Peptidyl-prolyl cis-trans isomerase A</name>
        <supramolecule_list>
            <complex_supramolecule supramolecule_id="1">
                <name>Peptidyl-prolyl cis-trans isomerase A</name>
                <parent>0</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>1</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <details>monomer</details>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                </natural_source>
            </complex_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>Peptidyl-prolyl cis-trans isomerase A</name>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.018036504</theoretical>
                </molecular_weight>
                <number_of_copies>1</number_of_copies>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="469008">Escherichia coli BL21(DE3)</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>MVNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYG
EKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIAD
CGQLE</string>
                    <external_references type="UNIPROTKB">P62937</external_references>
                </sequence>
                <ec_number>5.2.1.8</ec_number>
            </protein_or_peptide>
            <ligand macromolecule_id="2">
                <name>water</name>
                <molecular_weight>
                    <theoretical units="MDa">1.8015e-05</theoretical>
                </molecular_weight>
                <number_of_copies>32</number_of_copies>
                <formula>HOH</formula>
            </ligand>
        </macromolecule_list>
    </sample>
    <structure_determination_list>
        <structure_determination structure_determination_id="1">
            <method>electronCrystallography</method>
            <aggregation_state>threeDArray</aggregation_state>
            <specimen_preparation_list>
                <crystallography_preparation preparation_id="1">
                    <buffer>
                        <ph>7.5</ph>
                    </buffer>
                    <grid>
                        <details>unspecified</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                    </vitrification>
                    <crystal_formation>
                        <lipid_mixture>NA</lipid_mixture>
                        <temperature units="K">296.0</temperature>
                        <details>600 uL of protein at 60 mg/mL was combined with 400 uL of 50 percent PEG 3350 in a glass vial  and stirred with an Octagon stir bar at 500 RPM</details>
                    </crystal_formation>
                </crystallography_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <crystallography_microscopy microscopy_id="1">
                    <microscope>FEI TALOS ARCTICA</microscope>
                    <illumination_mode>OTHER</illumination_mode>
                    <imaging_mode>DIFFRACTION</imaging_mode>
                    <electron_source>FIELD EMISSION GUN</electron_source>
                    <acceleration_voltage units="kV">200</acceleration_voltage>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>TVIPS TEMCAM-F416 (4k x 4k)</film_or_detector_model>
                            <number_grids_imaged>1</number_grids_imaged>
                            <average_electron_dose_per_image units="e/Å^2">0.06</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                    <camera_length units="mm">2055</camera_length>
                </crystallography_microscopy>
            </microscopy_list>
            <crystallography_processing image_processing_id="1">
                <image_recording_id>1</image_recording_id>
                <final_reconstruction>
                    <resolution units="Å" res_type="BY AUTHOR">2.5</resolution>
                    <resolution_method>DIFFRACTION PATTERN/LAYERLINES</resolution_method>
                    <software_list>
                        <software>
                            <name>PHENIX</name>
                            <version>dev2880</version>
                        </software>
                    </software_list>
                </final_reconstruction>
                <molecular_replacement>
                    <software_list>
                        <software>
                            <name>PHENIX</name>
                            <version>dev2880</version>
                            <processing_details>PHASER</processing_details>
                        </software>
                    </software_list>
                </molecular_replacement>
                <crystallography_statistics>
                    <number_intensities_measured>22370</number_intensities_measured>
                    <number_structure_factors>6236</number_structure_factors>
                    <fourier_space_coverage>86.0</fourier_space_coverage>
                    <r_sym>0.217</r_sym>
                    <r_merge>0.217</r_merge>
                    <overall_phase_error>23.06</overall_phase_error>
                    <overall_phase_residual>23.059999999999999</overall_phase_residual>
                    <phase_error_rejection_criteria>0</phase_error_rejection_criteria>
                    <high_resolution units="Å">2.5</high_resolution>
                    <shell_list>
                        <shell shell_id="1">
                            <high_resolution units="Å">3.6045</high_resolution>
                            <low_resolution units="Å">30.4934</low_resolution>
                            <number_structure_factors>3581</number_structure_factors>
                            <phase_residual>14.449999999999999</phase_residual>
                            <fourier_space_coverage>84.0</fourier_space_coverage>
                            <multiplicity>3.41</multiplicity>
                        </shell>
                        <shell shell_id="2">
                            <high_resolution units="Å">2.8617</high_resolution>
                            <low_resolution units="Å">3.6045</low_resolution>
                            <number_structure_factors>3719</number_structure_factors>
                            <phase_residual>22.050000000000001</phase_residual>
                            <fourier_space_coverage>87.0</fourier_space_coverage>
                            <multiplicity>3.64</multiplicity>
                        </shell>
                        <shell shell_id="3">
                            <high_resolution units="Å">2.5002</high_resolution>
                            <low_resolution units="Å">2.8617</low_resolution>
                            <number_structure_factors>3746</number_structure_factors>
                            <phase_residual>32.299999999999997</phase_residual>
                            <fourier_space_coverage>87.0</fourier_space_coverage>
                            <multiplicity>3.72</multiplicity>
                        </shell>
                    </shell_list>
                </crystallography_statistics>
            </crystallography_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="2231">
        <file>emd_20645.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>82</col>
            <row>80</row>
            <sec>85</sec>
        </dimensions>
        <origin>
            <col>-20</col>
            <row>-19</row>
            <sec>-38</sec>
        </origin>
        <spacing>
            <x>85</x>
            <y>80</y>
            <z>82</z>
        </spacing>
        <cell>
            <a units="Å">50.055653</a>
            <b units="Å">47.4664</b>
            <c units="Å">49.974083</c>
            <alpha units="deg">90.0</alpha>
            <beta units="deg">90.0</beta>
            <gamma units="deg">90.0</gamma>
        </cell>
        <axis_order>
            <fast>Z</fast>
            <medium>Y</medium>
            <slow>X</slow>
        </axis_order>
        <statistics>
            <minimum>-3.1042123</minimum>
            <maximum>5.7321124</maximum>
            <average>-0.007928065</average>
            <std>0.973654</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">0.58889</x>
            <y units="Å">0.59333</y>
            <z units="Å">0.60944</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>1.46</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-20645::::</label>
        <annotation_details>2mFo-DFc at 1.5 sigma</annotation_details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <initial_model>
                    <access_code>4YUM</access_code>
                    <chain>
                        <source_name>PDB</source_name>
                        <initial_model_type>experimental model</initial_model_type>
                    </chain>
                </initial_model>
                <refinement_space>RECIPROCAL</refinement_space>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>
