<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" emdb_id="EMD-1494" version="3.0.1.1" 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>PDBe</processing_site>
      </current_status>
      <sites>
         <deposition>PDBe</deposition>
         <last_processing>PDBe</last_processing>
      </sites>
      <key_dates>
         <deposition>2008-03-11</deposition>
         <header_release>2008-03-11</header_release>
         <map_release>2009-03-31</map_release>
         <update>2012-10-24</update>
      </key_dates>
      <title>Structural Analysis of the Saf Pilus by Electron Microscopy and Image Processing. 3D reconstruction of the Type A Saf pilus, one of two conformations of the pilus refined.</title>
      <authors_list>
         <author>Salih O</author>
         <author>Remaut H</author>
         <author>Waksman G</author>
         <author>Orlova EV</author>
      </authors_list>
      <keywords>Pilus, electron microscopy, image processing, single-particle analysis, atomic structure fitting</keywords>
   </admin>
   <crossreferences>
      <citation_list>
         <primary_citation>
            <journal_citation published="true">
               <author order="1">Salih O</author>
               <author order="2">Remaut H</author>
               <author order="3">Waksman G</author>
               <author order="4">Orlova EV</author>
               <title>Structural analysis of the Saf pilus by electron microscopy and image processing.</title>
               <journal>J.MOL.BIOL.</journal>
               <volume>379</volume>
               <first_page>174</first_page>
               <last_page>187</last_page>
               <year>2008</year>
               <external_references type="PUBMED">18448124</external_references>
               <external_references type="DOI">doi:10.1016/j.jmb.2008.03.056</external_references>
            </journal_citation>
         </primary_citation>
      </citation_list>
      <pdb_list>
         <pdb_reference>
            <pdb_id>3cre</pdb_id>
            <relationship>
               <in_frame>FULLOVERLAP</in_frame>
            </relationship>
         </pdb_reference>
      </pdb_list>
   </crossreferences>
   <sample>
      <name>Saf pilus</name>
      <supramolecule_list>
         <sample_supramolecule supramolecule_id="1000">
            <name>Saf pilus</name>
            <number_unique_components>1</number_unique_components>
            <molecular_weight>
               <theoretical units="MDa">0.014</theoretical>
            </molecular_weight>
         </sample_supramolecule>
      </supramolecule_list>
      <macromolecule_list>
         <protein_or_peptide macromolecule_id="1">
            <name synonym="SafA pilus subunit">Wild-type SafA</name>
            <natural_source database="NCBI">
               <organism ncbi="99287">Salmonella enterica subsp. enterica serovar Typhimurium str. LT2</organism>
               <strain>LT2</strain>
               <cellular_location>Cell surface</cellular_location>
            </natural_source>
            <molecular_weight>
               <experimental units="MDa">0.0144</experimental>
            </molecular_weight>
            <oligomeric_state>Fibre</oligomeric_state>
            <recombinant_exp_flag>true</recombinant_exp_flag>
            <recombinant_expression database="NCBI">
               <recombinant_organism>Escherichia coli C600</recombinant_organism>
               <recombinant_plasmid>pTrc 99a</recombinant_plasmid>
            </recombinant_expression>
            <sequence>
               </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</concentration>
               <buffer>
                  <ph>8.0</ph>
                  <details>10 mM TRIS-HCl (pH 8) and 10 mM NaCl</details>
               </buffer>
               <staining>
                  <type>NEGATIVE</type>
                  <details>2% ammonium molybdate for 5 seconds</details>
               </staining>
               <grid>
                  <details>Continuous-carbon film</details>
               </grid>
               <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>TUNGSTEN HAIRPIN</electron_source>
               <acceleration_voltage units="kV">100</acceleration_voltage>
               <nominal_cs units="mm">2.4</nominal_cs>
               <nominal_defocus_min units="&#181;m">0.4</nominal_defocus_min>
               <nominal_defocus_max units="&#181;m">0.9</nominal_defocus_max>
               <nominal_magnification>44000.0</nominal_magnification>
               <specimen_holder_model>OTHER</specimen_holder_model>
               <image_recording_list>
                  <image_recording>
                     <film_or_detector_model category="FILM">KODAK SO-163 FILM</film_or_detector_model>
                     <digitization_details>
                        <scanner>ZEISS SCAI</scanner>
                        <sampling_interval units="&#181;m">1.591</sampling_interval>
                     </digitization_details>
                     <number_real_images>140</number_real_images>
                     <average_electron_dose_per_image units="e/&#8491;^2">25</average_electron_dose_per_image>
                     <od_range>1.5</od_range>
                     <bits_per_pixel>8.</bits_per_pixel>
                  </image_recording>
               </image_recording_list>
               <specimen_holder>Eucentric</specimen_holder>
            </single_particle_microscopy>
         </microscopy_list>
         <singleparticle_processing image_processing_id="1">
            <final_reconstruction>
               <applied_symmetry>
                  <point_group>C1</point_group>
               </applied_symmetry>
               <algorithm>OTHER</algorithm>
               <resolution res_type="BY AUTHOR" units="&#8491;">17.0</resolution>
               <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
               <software_list>
                  <software>
                     <name>Imagic</name>
                  </software>
               </software_list>
               <number_images_used>5000</number_images_used>
            </final_reconstruction>
            <final_angle_assignment>
               <details>Imagic: alpha, beta, gamma</details>
            </final_angle_assignment>
            <final_two_d_classification>
               <number_classes>247</number_classes>
            </final_two_d_classification>
         </singleparticle_processing>
      </structure_determination>
   </structure_determination_list>
   <map format="CCP4" size_kbytes="8193">
      <file>emd_1494.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;">203.648</a>
         <b units="&#8491;">203.648</b>
         <c units="&#8491;">203.648</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>-11.4216</minimum>
         <maximum>124.739000000000004</maximum>
         <average>0.00404985</average>
         <std>2.95342</std>
      </statistics>
      <pixel_spacing>
         <x units="&#8491;">1.591</x>
         <y units="&#8491;">1.591</y>
         <z units="&#8491;">1.591</z>
      </pixel_spacing>
      <contour_list>
         <contour primary="true">
            <level>2.95</level>
         </contour>
      </contour_list>
      <annotation_details>3D reconstruction of the Type A Saf pilus</annotation_details>
      <details>::::EMDATABANK.org::::EMD-1494::::</details>
   </map>
   <interpretation>
      <modelling_list>
         <modelling>
            <initial_model>
               <access_code>2CO4</access_code>
            </initial_model>
            <refinement_protocol>RIGID BODY FIT</refinement_protocol>
            <software_list>
               <software>
                  <name>URO</name>
               </software>
            </software_list>
            <details>Protocol: Rigid body</details>
            <target_criteria>Correlation coefficient</target_criteria>
            <refinement_space>RECIPROCAL</refinement_space>
         </modelling>
      </modelling_list>
   </interpretation>
</emd>