2026-01-28 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY RCSB RCSB 2025-12-28 2026-01-28 2026-01-28 2026-01-28 Not funded 12.7-Angstrom resolution structure of bacteriophage Sf6 in the C1 symmetry by cryo-electron tomography and sub-tomogram averaging with 538 particles reveal the tail appendage Tang L bacteriophage, shigella, podovirus, VIRUS Tang L 12.7-Angstrom resolution structure of bacteriophage Sf6 in the C1 symmetry by cryo-electron tomography and sub-tomogram averaging with 538 particles reveals the tail appendage To Be Published 0353 EMD-73070 other EM volume
structure by applying the icosahedral symmetry
 EMDB EMD-73070 other EM volume
structure by applying the icosahedral symmetry
 EMDB EMD-74840 associated EM volume Shigella phage Sf6 Shigella phage Sf6 0 1
complete virion purified from infected Shigella hosts
Shigella phage Sf6 Shigella flexneri 19 gp5 690.0 7 VIRION SPECIES false false subtomogramAveraging particle 5 7.4 10.0 Tris-HCl 1.0 MgCl2 C-flat GOLD 300 CARBON HOLEY PLASMA CLEANING OTHER ETHANE 100 277 FEI VITROBOT MARK IV FEI TALOS ARCTICA FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 1.0 6.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K3 BIOQUANTUM (6k x 4k) 5760 4092 1 0.4 3.0
11 tilt series were collected.
 1 C1 BACK PROJECTION 12.7 FSC 0.143 CUT-OFF RELION 5
The reconstruction was done with the C1 symmetry.
538 11 637 ab initio model from manually picked particles template matching RELION 5 EMAN2 2.99
A small set (~30) of particles were manually picked from a tilt series with EMAN2, which were used to generate an ab initial model. This model was used to pick particles in all tilt series by template matching with EMAN2. Particle coordinates were exported to Relion 5.
 CTFFIND 4.1.5
CTF correction was done with CtfFind4.1.5 wrapped in Relion5.
PHASE FLIPPING AND AMPLITUDE CORRECTION 1 RELION 5
All particles were classified into the best 3D class.
 MAXIMUM LIKELIHOOD RELION 5
Alignment was first performed with the icosahedral symmetry with rtf refinement and bayesian polishing. The angles were then expanded to the C1 symmetry with the region 5 symmetry_expand program, followed by 3D classification focused on a 5-fold vertex of the icosahedral phage particle using a manually generated smooth ellipsoidal mask. This generated a set of angles with the tail aligned to the same single 5-fold vertex, which then were used to reconstruct the phage particle in the C1 symmetry.
 emd_74840.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 1656.576 1656.576 1656.576 90.0 90.0 90.0 X Y Z -0.15535519 0.37923038 0.0013162496 0.013885863 4.314 4.314 4.314 0.09 AUTHOR masked map after post processing 5L35 Other experimental model
models from 5L35 were fitted into the map
 RIGID BODY FIT emd_74840_msk_1.map emd_74840_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 1656.576 1656.576 1656.576 90.0 90.0 90.0 X Y Z -0.19158195 0.37923038 0.000000000000321 0.029942028 4.314 4.314 4.314 AUTHOR unmasked map after post processing emd_74840_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 1656.576 1656.576 1656.576 90.0 90.0 90.0 X Y Z -0.4809325 0.5616801 -0.000000000000198 0.06190516 4.314 4.314 4.314 AUTHOR merged map from a relion reconstruct job emd_74840_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 1656.576 1656.576 1656.576 90.0 90.0 90.0 X Y Z -0.6689343 0.7524538 0.000000000000635 0.086760655 4.314 4.314 4.314 AUTHOR half map from a relion reconstruct job emd_74840_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 1656.576 1656.576 1656.576 90.0 90.0 90.0 X Y Z -0.6974828 0.75944185 0.000000000000127 0.09098134 4.314 4.314 4.314 AUTHOR half map from a relion reconstruct job