<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" emdb_id="EMD-1048" 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>2003-05-19</deposition>
         <header_release>2003-05-19</header_release>
         <map_release>2003-09-19</map_release>
         <update>2012-10-24</update>
      </key_dates>
      <title>Three-dimensional structure of bacteriophage T4 baseplate.</title>
      <authors_list>
         <author>Kostyuchenko VA</author>
         <author>Leiman PG</author>
         <author>Chipman PR</author>
         <author>Kanamaru S</author>
         <author>vanRaaij MJ</author>
         <author>Arisaka F</author>
         <author>Mesyanzhinov VV</author>
         <author>Rossmann MG</author>
      </authors_list>
      <keywords>
         </keywords>
   </admin>
   <crossreferences>
      <citation_list>
         <primary_citation>
            <journal_citation published="true">
               <author order="1">Kostyuchenko VA</author>
               <author order="2">Leiman PG</author>
               <author order="3">Chipman PR</author>
               <author order="4">Kanamaru S</author>
               <author order="5">van Raaij MJ</author>
               <author order="6">Arisaka F</author>
               <author order="7">Mesyanzhinov VV</author>
               <author order="8">Rossmann MG</author>
               <title>Three-dimensional structure of bacteriophage T4 baseplate.</title>
               <journal>NAT.STRUCT.BIOL.</journal>
               <volume>10</volume>
               <first_page>688</first_page>
               <last_page>693</last_page>
               <year>2003</year>
               <external_references type="PUBMED">12923574</external_references>
               <external_references type="DOI">doi:10.1038/nsb970</external_references>
            </journal_citation>
         </primary_citation>
      </citation_list>
      <pdb_list>
         <pdb_reference>
            <pdb_id>1pdf</pdb_id>
            <relationship>
               <in_frame>FULLOVERLAP</in_frame>
            </relationship>
         </pdb_reference>
         <pdb_reference>
            <pdb_id>1pdi</pdb_id>
            <relationship>
               <in_frame>FULLOVERLAP</in_frame>
            </relationship>
         </pdb_reference>
         <pdb_reference>
            <pdb_id>1pdj</pdb_id>
            <relationship>
               <in_frame>FULLOVERLAP</in_frame>
            </relationship>
         </pdb_reference>
         <pdb_reference>
            <pdb_id>1pdl</pdb_id>
            <relationship>
               <in_frame>FULLOVERLAP</in_frame>
            </relationship>
         </pdb_reference>
         <pdb_reference>
            <pdb_id>1pdm</pdb_id>
            <relationship>
               <in_frame>FULLOVERLAP</in_frame>
            </relationship>
         </pdb_reference>
         <pdb_reference>
            <pdb_id>1pdp</pdb_id>
            <relationship>
               <in_frame>FULLOVERLAP</in_frame>
            </relationship>
         </pdb_reference>
         <pdb_reference>
            <pdb_id>2fl8</pdb_id>
            <relationship>
               <in_frame>FULLOVERLAP</in_frame>
            </relationship>
         </pdb_reference>
         <pdb_reference>
            <pdb_id>3h3w</pdb_id>
            <relationship>
               <in_frame>FULLOVERLAP</in_frame>
            </relationship>
         </pdb_reference>
      </pdb_list>
   </crossreferences>
   <sample>
      <name>Bacteriophage T4 baseplate-tail tube assembly</name>
      <supramolecule_list>
         <sample_supramolecule supramolecule_id="1000">
            <name>Bacteriophage T4 baseplate-tail tube assembly</name>
            <oligomeric_state>the complex has sixfold symmetry</oligomeric_state>
            <number_unique_components>1</number_unique_components>
         </sample_supramolecule>
      </supramolecule_list>
      <macromolecule_list>
         <protein_or_peptide macromolecule_id="1">
            <name>baseplate-tail tube complex</name>
            <natural_source database="NCBI">
               <organism ncbi="10665">Enterobacteria phage T4</organism>
               <strain>T4 18-,23-</strain>
               <synonym_organism>bacteriophage T4</synonym_organism>
               <organelle>baseplate and tail tube</organelle>
            </natural_source>
            <recombinant_exp_flag>true</recombinant_exp_flag>
            <recombinant_expression database="NCBI">
               <recombinant_organism>Escherichia coli BE</recombinant_organism>
            </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">5</concentration>
               <buffer>
                  <ph>7.0</ph>
                  <details>water</details>
               </buffer>
               <grid>
                  <details>holey carbon</details>
               </grid>
               <vitrification>
                  <cryogen_name>ETHANE</cryogen_name>
                  <method>Blot for 2 seconds before plunging</method>
               </vitrification>
            </single_particle_preparation>
         </specimen_preparation_list>
         <microscopy_list>
            <single_particle_microscopy microscopy_id="1">
               <microscope>FEI/PHILIPS CM300FEG/T</microscope>
               <illumination_mode>FLOOD BEAM</illumination_mode>
               <imaging_mode>BRIGHT FIELD</imaging_mode>
               <electron_source>FIELD EMISSION GUN</electron_source>
               <acceleration_voltage units="kV">300</acceleration_voltage>
               <nominal_cs units="mm">2</nominal_cs>
               <nominal_defocus_min units="&#181;m">1.2</nominal_defocus_min>
               <nominal_defocus_max units="&#181;m">5.0</nominal_defocus_max>
               <nominal_magnification>45000.0</nominal_magnification>
               <calibrated_magnification>47000.0</calibrated_magnification>
               <specimen_holder_model>GATAN LIQUID NITROGEN</specimen_holder_model>
               <date>2001-01-30</date>
               <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">14</sampling_interval>
                     </digitization_details>
                     <number_real_images>15</number_real_images>
                     <average_electron_dose_per_image units="e/&#8491;^2">25</average_electron_dose_per_image>
                     <details>images were scanned at 7 micron per pixel and averaged
        2x2       to give 14 micron per pixel</details>
                     <bits_per_pixel>8.</bits_per_pixel>
                  </image_recording>
               </image_recording_list>
               <specimen_holder>626 Single Tilt Cryotransfer System</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">
            <ctf_correction>
               <details>each particle</details>
            </ctf_correction>
            <final_reconstruction>
               <applied_symmetry>
                  <point_group>C6</point_group>
               </applied_symmetry>
               <algorithm>OTHER</algorithm>
               <resolution res_type="BY AUTHOR" units="&#8491;">12.0</resolution>
               <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
               <software_list>
                  <software>
                     <name>SPIDER</name>
                  </software>
               </software_list>
               <details>modified SPIDER version was used to allow reconstruction  of the whole baseplate-tail tube assembly</details>
               <number_images_used>945</number_images_used>
            </final_reconstruction>
         </singleparticle_processing>
      </structure_determination>
   </structure_determination_list>
   <map format="CCP4" size_kbytes="29414">
      <file>emd_1048.map.gz</file>
      <symmetry>
         <space_group>1</space_group>
      </symmetry>
      <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
      <dimensions>
         <col>196</col>
         <row>196</row>
         <sec>196</sec>
      </dimensions>
      <origin>
         <col>-98</col>
         <row>-98</row>
         <sec>-97</sec>
      </origin>
      <spacing>
         <x>196</x>
         <y>196</y>
         <z>196</z>
      </spacing>
      <cell>
         <a units="&#8491;">583.8291</a>
         <b units="&#8491;">583.8291</b>
         <c units="&#8491;">583.8291</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>-7.64827013</minimum>
         <maximum>10.344811440000001</maximum>
         <average>0.0</average>
         <std>1.0</std>
      </statistics>
      <pixel_spacing>
         <x units="&#8491;">2.97872</x>
         <y units="&#8491;">2.97872</y>
         <z units="&#8491;">2.97872</z>
      </pixel_spacing>
      <contour_list>
         <contour primary="true">
            <level>1.45</level>
            <source>AUTHOR</source>
         </contour>
      </contour_list>
      <annotation_details>map contains the baseplate and the proximal
 part of the tail tube</annotation_details>
      <details>::::EMDATABANK.org::::EMD-1048::::</details>
   </map>
   <interpretation>
      <modelling_list>
         <modelling>
            <refinement_protocol>RIGID BODY FIT</refinement_protocol>
            <software_list>
               <software>
                  <name>Situs 2.0, Colores</name>
               </software>
            </software_list>
            <details>Protocol: laplacian filtered real space</details>
            <target_criteria>correlation coefficient</target_criteria>
            <refinement_space>REAL</refinement_space>
         </modelling>
         <modelling>
            <refinement_protocol>RIGID BODY FIT</refinement_protocol>
            <software_list>
               <software>
                  <name>Situs 2.0, Colores</name>
               </software>
            </software_list>
            <details>Protocol: laplacian filtered real space</details>
            <target_criteria>correlation coefficient</target_criteria>
            <refinement_space>REAL</refinement_space>
         </modelling>
         <modelling>
            <refinement_protocol>RIGID BODY FIT</refinement_protocol>
            <software_list>
               <software>
                  <name>Situs 2.0, Colores</name>
               </software>
            </software_list>
            <details>Protocol: laplacian filtered real space</details>
            <target_criteria>correlation coefficient</target_criteria>
            <refinement_space>REAL</refinement_space>
         </modelling>
         <modelling>
            <refinement_protocol>RIGID BODY FIT</refinement_protocol>
            <software_list>
               <software>
                  <name>Situs 2.0, Colores</name>
               </software>
            </software_list>
            <details>Protocol: laplacian filtered real space</details>
            <target_criteria>correlation coefficient</target_criteria>
            <refinement_space>REAL</refinement_space>
         </modelling>
         <modelling>
            <refinement_protocol>RIGID BODY FIT</refinement_protocol>
            <software_list>
               <software>
                  <name>Situs 2.0, Colores</name>
               </software>
            </software_list>
            <details>Protocol: laplacian filtered real space</details>
            <target_criteria>correlation coefficient</target_criteria>
            <refinement_space>REAL</refinement_space>
         </modelling>
         <modelling>
            <refinement_protocol>RIGID BODY FIT</refinement_protocol>
            <software_list>
               <software>
                  <name>Situs 2.0, Colores</name>
               </software>
            </software_list>
            <details>Protocol: laplacian filtered real space</details>
            <target_criteria>correlation coefficient</target_criteria>
            <refinement_space>REAL</refinement_space>
         </modelling>
         <modelling>
            <refinement_protocol>RIGID BODY FIT</refinement_protocol>
            <software_list>
               <software>
                  <name>Situs 2.0, Colores</name>
               </software>
            </software_list>
            <details>Protocol: laplacian filtered real space</details>
            <target_criteria>correlation coefficient</target_criteria>
            <refinement_space>REAL</refinement_space>
         </modelling>
         <modelling>
            <refinement_protocol>RIGID BODY FIT</refinement_protocol>
            <software_list>
               <software>
                  <name>Situs 2.0, Colores</name>
               </software>
            </software_list>
            <details>Protocol: laplacian filtered real space</details>
            <target_criteria>correlation coefficient</target_criteria>
            <refinement_space>REAL</refinement_space>
         </modelling>
      </modelling_list>
   </interpretation>
</emd>