<emd emdb_id="EMD-5339" 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>2011-08-30</deposition>
            <header_release>2011-11-28</header_release>
            <map_release>2011-11-29</map_release>
            <update>2011-11-29</update>
        </key_dates>
        <title>Amplitude corrected and filtered map of GroEL obtained with a DDD camera to compare results from cryo SPA with a CCD camera using the same grid. Initial evaluation of a Direct Detection Device detector for single particle cryo-electron microscopy.</title>
        <authors_list>
            <author>Milazzo AC</author>
            <author>Cheng A</author>
            <author>Moeller A</author>
            <author>Lyumkis D</author>
            <author>Jacovetty E</author>
            <author>Polukas J</author>
            <author>Ellisman MH</author>
            <author>Xuong NH</author>
            <author>Carragher B</author>
            <author>Potter CS</author>
        </authors_list>
        <keywords>GroEL</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Milazzo AC</author>
                    <author order="2">Cheng A</author>
                    <author order="3">Moeller A</author>
                    <author order="4">Lyumkis D</author>
                    <author order="5">Jacovetty E</author>
                    <author order="6">Polukas J</author>
                    <author order="7">Ellisman MH</author>
                    <author order="8">Xuong NH</author>
                    <author order="9">Carragher B</author>
                    <author order="10">Potter CS</author>
                    <title>Initial evaluation of a direct detection device detector for single particle cryo-electron microscopy.</title>
                    <journal>J.STRUCT.BIOL.</journal>
                    <volume>176</volume>
                    <first_page>404</first_page>
                    <last_page>408</last_page>
                    <year>2011</year>
                    <external_references type="PUBMED">21933715</external_references>
                    <external_references type="DOI">doi:10.1016/j.jsb.2011.09.002</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>GroEL</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>GroEL</name>
                <oligomeric_state>D7 14-mer</oligomeric_state>
                <number_unique_components>1</number_unique_components>
                <molecular_weight>
                    <experimental units="MDa">0.8</experimental>
                    <theoretical units="MDa">0.8</theoretical>
                </molecular_weight>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name synonym="GroEL">GroEL</name>
                <natural_source database="NCBI">
                    <organism ncbi="562">Escherichia coli</organism>
                </natural_source>
                <molecular_weight>
                    <experimental units="MDa">0.8</experimental>
                    <theoretical units="MDa">0.8</theoretical>
                </molecular_weight>
                <number_of_copies>1</number_of_copies>
                <oligomeric_state>homotetradecamer</oligomeric_state>
                <recombinant_exp_flag>true</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>particle</aggregation_state>
            <specimen_preparation_list>
                <single_particle_preparation preparation_id="1">
                    <concentration units="mg/mL">1.5</concentration>
                    <buffer>
                        <ph>7.5</ph>
                        <details>100mM HEPES, 10mM Mg(OAc)2, 10mM KOAc, 2mM DTT</details>
                    </buffer>
                    <grid>
                        <details>Protochips C-flat grid, holey carbon with 2um holes and 2um spacing 400 mesh copper grid</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">100</chamber_humidity>
                        <chamber_temperature units="K">93</chamber_temperature>
                        <instrument>OTHER</instrument>
                        <details>Vitrification instrument: Vitrobot. Grid plasma cleaned for 20 seconds with Fischione 1020 plasma cleaner using 75 percent argon, 25 percent oxygen mix.</details>
                        <method>Temperature of chamber was 4 degrees C. 0 seconds drain time. Single blot. 0 mm offset. 4 uL sample applied to grid. Blot for 3.5 seconds before plunging.</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_cs units="mm">2</nominal_cs>
                    <nominal_defocus_min units="&#181;m">0.8</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">2.5</nominal_defocus_max>
                    <nominal_magnification>29000.0</nominal_magnification>
                    <calibrated_magnification>43796.0</calibrated_magnification>
                    <specimen_holder_model>GATAN LIQUID NITROGEN</specimen_holder_model>
                    <temperature>
                        <temperature_min units="K">102</temperature_min>
                        <temperature_max units="K">102</temperature_max>
                        <temperature_average units="K">102</temperature_average>
                    </temperature>
                    <alignment_procedure>
                        <legacy>
                            <astigmatism>The objective lens astigmatism was corrected automatically using Leginon</astigmatism>
                            <electron_beam_tilt_params>beam tilt was less than 0.1 mrad</electron_beam_tilt_params>
                        </legacy>
                    </alignment_procedure>
                    <date>2011-02-24</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">DIRECT ELECTRON DE-12 (4k x 3k)</film_or_detector_model>
                            <number_real_images>2313</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">20</average_electron_dose_per_image>
                            <bits_per_pixel>16.</bits_per_pixel>
                        </image_recording>
                    </image_recording_list>
                    <specimen_holder>Gatan side-entry 626 cryostage</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>CTF correction of each particle</details>
                </ctf_correction>
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">6.7</resolution>
                    <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>XMIPP</name>
                        </software>
                    </software_list>
                    <details>Amplitude corrected with an x-ray scattering curve to 5A and low pass filtered to 6A</details>
                    <number_images_used>30711</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="27649">
        <file>emd_5339.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>192</col>
            <row>192</row>
            <sec>192</sec>
        </dimensions>
        <origin>
            <col>-96</col>
            <row>-96</row>
            <sec>-96</sec>
        </origin>
        <spacing>
            <x>192</x>
            <y>192</y>
            <z>192</z>
        </spacing>
        <cell>
            <a units="&#8491;">263.04</a>
            <b units="&#8491;">263.04</b>
            <c units="&#8491;">263.04</c>
            <alpha units="deg">90</alpha>
            <beta units="deg">90</beta>
            <gamma units="deg">90</gamma>
        </cell>
        <axis_order>
            <fast>X</fast>
            <medium>Y</medium>
            <slow>Z</slow>
        </axis_order>
        <statistics>
            <minimum>-8.552670000000001</minimum>
            <maximum>8.80916</maximum>
            <average>0.00000000442695</average>
            <std>1.0</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">1.37</x>
            <y units="&#8491;">1.37</y>
            <z units="&#8491;">1.37</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>1.88</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Filtered map of GroEL with DDD camera.</annotation_details>
        <details>::::EMDATABANK.org::::EMD-5339::::</details>
    </map>
</emd>