<emd emdb_id="EMD-6313" 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>2015-03-27</deposition>
            <header_release>2015-04-08</header_release>
            <map_release>2015-04-08</map_release>
            <update>2015-04-08</update>
        </key_dates>
        <title>2.5A structure of lysozyme solved by MicroED</title>
        <authors_list>
            <author>Nannenga BL</author>
            <author>Shi D</author>
            <author>Leslie AGW</author>
            <author>Gonen T</author>
        </authors_list>
        <keywords>lysozyme, microcrystal</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Nannenga BL</author>
                    <author order="2">Shi D</author>
                    <author order="3">Leslie AG</author>
                    <author order="4">Gonen T</author>
                    <title>High-resolution structure determination by continuous-rotation data collection in MicroED</title>
                    <journal>Nature Methods</journal>
                    <volume>11</volume>
                    <first_page>927</first_page>
                    <last_page>930</last_page>
                    <year>2014</year>
                    <external_references type="PUBMED">25086503</external_references>
                    <external_references type="DOI">doi:10.1038/nmeth.3043</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>3j6k</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>Hen egg white lysozyme</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Hen egg white lysozyme</name>
                <details>lysozyme microcrystals</details>
                <oligomeric_state>1</oligomeric_state>
                <number_unique_components>1</number_unique_components>
                <molecular_weight>
                    <theoretical units="MDa">0.0143</theoretical>
                </molecular_weight>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name synonym="lysozyme">Lysozyme C</name>
                <natural_source database="NCBI">
                    <organism ncbi="9031">Gallus gallus</organism>
                    <synonym_organism>Chicken</synonym_organism>
                    <tissue>egg white</tissue>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.0143</theoretical>
                </molecular_weight>
                <details>lysozyme microcrystals</details>
                <recombinant_exp_flag>false</recombinant_exp_flag>
                <recombinant_expression database="NCBI" />
                <sequence>
                    <external_references type="UNIPROTKB">P00698</external_references>
                </sequence>
            </protein_or_peptide>
        </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">200</concentration>
                    <buffer>
                        <ph>4.5</ph>
                        <details>50 mM sodium acetate, 3.5 M sodium chloride, 15% PEG5000</details>
                    </buffer>
                    <grid>
                        <details>300 mesh copper grid with holey carbon support</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_temperature units="K">100</chamber_temperature>
                        <instrument>FEI VITROBOT MARK IV</instrument>
                        <method>Add crystals to grid for 30 seconds and blot for 10-12 seconds.</method>
                    </vitrification>
                    <details>batch crystallization</details>
                    <crystal_formation>
                        <details>batch crystallization</details>
                    </crystal_formation>
                </crystallography_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <crystallography_microscopy microscopy_id="1">
                    <microscope>FEI TECNAI F20</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>
                    <specimen_holder_model>GATAN LIQUID NITROGEN</specimen_holder_model>
                    <temperature>
                        <temperature_min units="K">90</temperature_min>
                        <temperature_max units="K">110</temperature_max>
                        <temperature_average units="K">100</temperature_average>
                    </temperature>
                    <date>2014-02-04</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">TVIPS TEMCAM-F416 (4k x 4k)</film_or_detector_model>
                            <average_electron_dose_per_image units="e/&#8491;^2">0.1</average_electron_dose_per_image>
                            <detector_distance>1500</detector_distance>
                            <details>Raw diffraction images are available upon request. Contact the Gonen lab for access.</details>
                        </image_recording>
                    </image_recording_list>
                    <tilt_angle_min>-45</tilt_angle_min>
                    <tilt_angle_max>45</tilt_angle_max>
                    <tilt_series>
                        <axis1>
                            <min_angle units="deg">-45</min_angle>
                            <max_angle units="deg">45</max_angle>
                        </axis1>
                    </tilt_series>
                </crystallography_microscopy>
            </microscopy_list>
            <crystallography_processing image_processing_id="1">
                <final_reconstruction>
                    <resolution res_type="BY AUTHOR" units="&#8491;">2.5</resolution>
                    <resolution_method>DIFFRACTION PATTERN/LAYERLINES</resolution_method>
                </final_reconstruction>
                <crystal_parameters>
                    <unit_cell>
                        <a units="&#8491;">75.96</a>
                        <b units="&#8491;">75.96</b>
                        <c units="&#8491;">37.22</c>
                        <gamma units="deg">90</gamma>
                        <alpha units="deg">90</alpha>
                        <beta units="deg">90</beta>
                    </unit_cell>
                    <space_group>P 43 21 2</space_group>
                </crystal_parameters>
            </crystallography_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="3664">
        <file>emd_6313.map.gz</file>
        <symmetry>
            <space_group>96</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>60</col>
            <row>125</row>
            <sec>125</sec>
        </dimensions>
        <origin>
            <col>-60</col>
            <row>-125</row>
            <sec>-125</sec>
        </origin>
        <spacing>
            <x>125</x>
            <y>125</y>
            <z>60</z>
        </spacing>
        <cell>
            <a units="&#8491;">75.96</a>
            <b units="&#8491;">75.96</b>
            <c units="&#8491;">37.219982</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>-3.15723062</minimum>
            <maximum>5.18146324</maximum>
            <average>0.0</average>
            <std>1.0</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">0.60767996</x>
            <y units="&#8491;">0.60767996</y>
            <z units="&#8491;">0.620333</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>1.5</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Lysozyme electron diffraction phased by molecular replacement. PDB ID 3J6K.</annotation_details>
        <details>::::EMDATABANK.org::::EMD-6313::::</details>
    </map>
    <interpretation>
        <segmentation_list>
            <segmentation>
                <file>emd_6313_msk_1.map</file>
                <mask_details format="CCP4" size_kbytes="966">
                    <file>emd_6313_msk_1.map</file>
                    <symmetry>
                        <space_group>1</space_group>
                    </symmetry>
                    <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
                    <dimensions>
                        <col>67</col>
                        <row>67</row>
                        <sec>55</sec>
                    </dimensions>
                    <origin>
                        <col>-47</col>
                        <row>-36</row>
                        <sec>-62</sec>
                    </origin>
                    <spacing>
                        <x>67</x>
                        <y>55</y>
                        <z>67</z>
                    </spacing>
                    <cell>
                        <a units="&#8491;">33.4224</a>
                        <b units="&#8491;">40.71456</b>
                        <c units="&#8491;">41.562313</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>-3.15723062</minimum>
                        <maximum>5.18146324</maximum>
                        <average>-0.0061503</average>
                        <std>0.99229306</std>
                    </statistics>
                    <pixel_spacing>
                        <x units="&#8491;">0.60768</x>
                        <y units="&#8491;">0.60768</y>
                        <z units="&#8491;">0.620333</z>
                    </pixel_spacing>
                    <annotation_details>This mask represents the map masked around the asymmetric unit (PDB 3J6K)</annotation_details>
                    <details>::::EMDATABANK.org::::</details>
                </mask_details>
            </segmentation>
        </segmentation_list>
    </interpretation>
</emd>
