<emd emdb_id="EMD-5420" 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>2012-05-08</deposition>
            <header_release>2012-06-05</header_release>
            <map_release>2012-07-09</map_release>
            <update>2012-07-09</update>
        </key_dates>
        <title>Pyrococcus abyssi methylation-guide sRNP</title>
        <authors_list>
            <author>Bower-Phipps KR</author>
            <author>Taylor DW</author>
            <author>Wang HW</author>
            <author>Baserga SJ</author>
        </authors_list>
        <keywords>archaea, box C/D sRNP, single particle EM, rRNA modification, RNA-protein complex, non-coding RNA</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Bower-Phipps KR</author>
                    <author order="2">Taylor DW</author>
                    <author order="3">Wang HW</author>
                    <author order="4">Baserga SJ</author>
                    <title>The box C/D sRNP dimeric architecture is conserved across domain Archaea.</title>
                    <journal>RNA</journal>
                    <volume>18</volume>
                    <first_page>1527</first_page>
                    <last_page>1540</last_page>
                    <year>2012</year>
                    <external_references type="PUBMED">22753779</external_references>
                    <external_references type="DOI">doi:10.1261/rna.033134.112</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>Pyrococcus abyssi methylation-guide sRNP</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Pyrococcus abyssi methylation-guide sRNP</name>
                <oligomeric_state>Four copies of each box C/D core protein could be docked in this map.</oligomeric_state>
                <number_unique_components>1</number_unique_components>
                <molecular_weight>
                    <theoretical units="MDa">0.368</theoretical>
                </molecular_weight>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name synonym="box C/D sRNP">ribonucleoprotein</name>
                <natural_source database="NCBI">
                    <organism ncbi="29292">Pyrococcus abyssi</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.368</theoretical>
                </molecular_weight>
                <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">
                    <buffer>
                        <ph>7.5</ph>
                        <details>20mM HEPES, 500mM NaCl, 1.5mM MgCl2</details>
                    </buffer>
                    <staining>
                        <type>NEGATIVE</type>
                        <details>2% uranyl formate</details>
                    </staining>
                    <vitrification>
                        <cryogen_name>NONE</cryogen_name>
                        <instrument>OTHER</instrument>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>FEI TECNAI 12</microscope>
                    <illumination_mode>FLOOD BEAM</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>LAB6</electron_source>
                    <acceleration_voltage units="kV">120</acceleration_voltage>
                    <nominal_magnification>42000.0</nominal_magnification>
                    <specimen_holder_model>SIDE ENTRY, EUCENTRIC</specimen_holder_model>
                    <details>low-dose conditions</details>
                    <date>2011-09-08</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">GATAN ULTRASCAN 4000 (4k x 4k)</film_or_detector_model>
                            <average_electron_dose_per_image units="e/&#8491;^2">20</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">25.0</resolution>
                    <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>SPIDER</name>
                        </software>
                    </software_list>
                    <number_images_used>9248</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="8193">
        <file>emd_5420.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>128</col>
            <row>128</row>
            <sec>128</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>128</x>
            <y>128</y>
            <z>128</z>
        </spacing>
        <cell>
            <a units="&#8491;">345.6</a>
            <b units="&#8491;">345.6</b>
            <c units="&#8491;">345.6</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>-7.35317993</minimum>
            <maximum>17.610933299999999</maximum>
            <average>0.0</average>
            <std>0.99999976</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">2.7</x>
            <y units="&#8491;">2.7</y>
            <z units="&#8491;">2.7</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>3.0</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Projection matching single particle reconstruction of Pyrococcus abyssi box C/D sRNP, 25 Angstrom resolution</annotation_details>
        <details>::::EMDATABANK.org::::EMD-5420::::</details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <initial_model>
                    <access_code>3NMU</access_code>
                </initial_model>
                <software_list>
                    <software>
                        <name>Chimera, Situs</name>
                    </software>
                </software_list>
                <refinement_space>REAL</refinement_space>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>