<?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_3/emdb.xsd" version="3.0.9.3" emdb_id="EMD-25456">
    <admin>
        <current_status>
            <date>2024-11-06</date>
            <code>REL</code>
            <processing_site>RCSB</processing_site>
        </current_status>
        <sites>
            <deposition>RCSB</deposition>
            <last_processing>RCSB</last_processing>
        </sites>
        <key_dates>
            <deposition>2021-11-19</deposition>
            <header_release>2022-09-07</header_release>
            <map_release>2022-09-07</map_release>
            <update>2024-11-06</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>Howard Hughes Medical Institute (HHMI)</funding_body>
                <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>P41GM136508</code>
                <country>United States</country>
            </grant_reference>
        </grant_support>
        <title>MicroED structure of proteinase K from a 130 nm thick lamella measured at 120 kV</title>
        <authors_list>
            <author>Martynowycz MW</author>
            <author>Clabbers MTB</author>
        </authors_list>
        <keywords>Serine protease, HYDROLASE</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Martynowycz MW</author>
                    <author ORCID="0000-0002-5466-6508" order="2">Clabbers MTB</author>
                    <author ORCID="0000-0002-1077-8137" order="3">Unge J</author>
                    <author ORCID="0000-0002-8936-0912" order="4">Hattne J</author>
                    <author ORCID="0000-0002-9254-4069" order="5">Gonen T</author>
                    <title>Benchmarking the ideal sample thickness in cryo-EM.</title>
                    <journal_abbreviation>Proc.Natl.Acad.Sci.USA</journal_abbreviation>
                    <country>US</country>
                    <volume>118</volume>
                    <year>2021</year>
                    <external_references type="PUBMED">34873060</external_references>
                    <external_references type="DOI">doi:10.1073/pnas.2108884118</external_references>
                    <external_references type="ISSN">1091-6490</external_references>
                    <external_references type="CSD">0040</external_references>
                    <external_references type="ASTM">PNASA6</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>7svy</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>Proteinase K</name>
        <supramolecule_list>
            <complex_supramolecule supramolecule_id="1">
                <name>Proteinase K</name>
                <parent>0</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>1</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <details>Serine protease</details>
                <natural_source database="NCBI">
                    <organism ncbi="37998">Parengyodontium album</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.0289</theoretical>
                </molecular_weight>
            </complex_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>Proteinase K</name>
                <natural_source database="NCBI">
                    <organism ncbi="37998">Parengyodontium album</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.028930782999999998</theoretical>
                </molecular_weight>
                <number_of_copies>1</number_of_copies>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>AAQTNAPWGLARISSTSPGTSTYYYDESAGQGSCVYVIDTGIEASHPEFEGRAQMVKTYYYSSRDGNGHGTHCAGTVGSR
TYGVAKKTQLFGVKVLDDNGSGQYSTIIAGMDFVASDKNNRNCPKGVVASLSLGGGYSSSVNSAAARLQSSGVMVAVAAG
NNNADARNYSPASEPSVCTVGASDRYDRRSSFSNYGSVLDIFGPGTSILSTWIGGSTRSISGTSMATPHVAGLAAYLMTL
GKTTAASACRYIADTANKGDLSNIPFGTVNLLAYNNYQA</string>
                    <external_references type="UNIPROTKB">P06873</external_references>
                </sequence>
                <ec_number>3.4.21.64</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>23</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">
                    <concentration units="mg/mL">5</concentration>
                    <buffer>
                        <ph>7.5</ph>
                    </buffer>
                    <grid>
                        <model>Quantifoil R2/2</model>
                        <material>COPPER</material>
                        <mesh>200</mesh>
                        <support_film film_type_id="1">
                            <film_material>CARBON</film_material>
                            <film_topology>HOLEY</film_topology>
                            <film_thickness>10.0</film_thickness>
                        </support_film>
                        <pretreatment>
                            <type>GLOW DISCHARGE</type>
                            <time units="s">30</time>
                        </pretreatment>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">95</chamber_humidity>
                        <chamber_temperature units="K">277</chamber_temperature>
                        <instrument>LEICA PLUNGER</instrument>
                    </vitrification>
                    <details>Microcrystals</details>
                </crystallography_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <crystallography_microscopy microscopy_id="1">
                    <microscope>FEI TITAN KRIOS</microscope>
                    <illumination_mode>FLOOD BEAM</illumination_mode>
                    <imaging_mode>DIFFRACTION</imaging_mode>
                    <electron_source>FIELD EMISSION GUN</electron_source>
                    <acceleration_voltage units="kV">120</acceleration_voltage>
                    <c2_aperture_diameter units="µm">50.0</c2_aperture_diameter>
                    <nominal_cs units="mm">2.7</nominal_cs>
                    <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
                    <cooling_holder_cryogen>NITROGEN</cooling_holder_cryogen>
                    <temperature>
                        <temperature_min units="K">77.0</temperature_min>
                        <temperature_max units="K">90.0</temperature_max>
                    </temperature>
                    <alignment_procedure>
                        <basic/>
                    </alignment_procedure>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>FEI CETA (4k x 4k)</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>1</number_real_images>
                            <number_diffraction_images>120</number_diffraction_images>
                            <average_exposure_time units="s">1.0</average_exposure_time>
                            <average_electron_dose_per_image units="e/Å^2">0.01</average_electron_dose_per_image>
                            <details>0.5 degrees per second, 1 second readout, 30 to -30 degrees.</details>
                        </image_recording>
                    </image_recording_list>
                    <camera_length units="mm">1427</camera_length>
                </crystallography_microscopy>
            </microscopy_list>
            <crystallography_processing image_processing_id="1">
                <image_recording_id>1</image_recording_id>
                <details>Binned by 2.</details>
                <final_reconstruction>
                    <resolution_method>DIFFRACTION PATTERN/LAYERLINES</resolution_method>
                    <software_list>
                        <software>
                            <name>PHENIX</name>
                        </software>
                    </software_list>
                </final_reconstruction>
                <merging_software_list>
                    <software>
                        <name>AIMLESS</name>
                    </software>
                </merging_software_list>
                <crystallography_statistics>
                    <number_intensities_measured>49740</number_intensities_measured>
                    <number_structure_factors>8882</number_structure_factors>
                    <fourier_space_coverage>83.0</fourier_space_coverage>
                    <r_sym>15.0</r_sym>
                    <r_merge>33.0</r_merge>
                    <overall_phase_error>27</overall_phase_error>
                    <overall_phase_residual>0.0</overall_phase_residual>
                    <phase_error_rejection_criteria>None</phase_error_rejection_criteria>
                    <high_resolution units="Å">2.3</high_resolution>
                    <shell_list>
                        <shell shell_id="1">
                            <high_resolution units="Å">2.63</high_resolution>
                            <low_resolution units="Å">2.3</low_resolution>
                            <number_structure_factors>2741</number_structure_factors>
                            <phase_residual>31.0</phase_residual>
                            <fourier_space_coverage>82.0</fourier_space_coverage>
                            <multiplicity>5.0</multiplicity>
                        </shell>
                    </shell_list>
                </crystallography_statistics>
            </crystallography_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="3012">
        <file>emd_25456.map.gz</file>
        <symmetry>
            <space_group>96</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>90</col>
            <row>94</row>
            <sec>89</sec>
        </dimensions>
        <origin>
            <col>-47</col>
            <row>-77</row>
            <sec>-5</sec>
        </origin>
        <spacing>
            <x>120</x>
            <y>120</y>
            <z>180</z>
        </spacing>
        <cell>
            <a units="Å">66.838</a>
            <b units="Å">66.838</b>
            <c units="Å">100.502</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>-3.7998223</minimum>
            <maximum>4.9652925</maximum>
            <average>0.0015968971</average>
            <std>0.97468036</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">0.5569833</x>
            <y units="Å">0.5569833</y>
            <z units="Å">0.5583444</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>1.0</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-25456::::</label>
        <annotation_details>2Fo-Fc MicroED map from a 130nm thick lamellae measured at 120kV</annotation_details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <initial_model>
                    <access_code>6CL7</access_code>
                    <chain>
                        <chain_id>A</chain_id>
                        <residue_range>106-384</residue_range>
                        <source_name>PDB</source_name>
                        <initial_model_type>experimental model</initial_model_type>
                    </chain>
                </initial_model>
                <refinement_protocol>RIGID BODY FIT</refinement_protocol>
                <target_criteria>Maximum liklihood</target_criteria>
                <refinement_space>RECIPROCAL</refinement_space>
                <overall_bvalue>34.0</overall_bvalue>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>
