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In situ structure of the Vaccinia virus (WR) A4/A10 palisade trimer in mature virions by flexible fitting into a cryoET map
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Refinement RMS Deviations Key Refinement Restraint Deviation r_lrange_it 194.4 r_lrange_other 194.399 r_mcangle_it 89.897 r_mcangle_other 89.892 r_scangle_it 78.4 r_scangle_other 78.397 r_mcbond_it 50.091 r_mcbond_other 50.091 r_scbond_it 39.297 r_scbond_other 39.295
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 194.4 r_lrange_other 194.399 r_mcangle_it 89.897 r_mcangle_other 89.892 r_scangle_it 78.4 r_scangle_other 78.397 r_mcbond_it 50.091 r_mcbond_other 50.091 r_scbond_it 39.297 r_scbond_other 39.295 r_dihedral_angle_3_deg 17.147 r_dihedral_angle_6_deg 16.339 r_dihedral_angle_2_deg 8.436 r_dihedral_angle_1_deg 6.532 r_angle_refined_deg 1.547 r_angle_other_deg 0.52 r_nbd_refined 0.218 r_symmetry_nbd_other 0.189 r_nbtor_refined 0.17 r_xyhbond_nbd_refined 0.082 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.065 r_symmetry_xyhbond_nbd_other 0.021 r_gen_planes_refined 0.009 r_bond_refined_d 0.006 r_gen_planes_other 0.001 r_bond_other_d
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SUBTOMOGRAM AVERAGING Number of Particles 123492 Reported Resolution (Å) 9.7 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C3
Map-Model Fitting and Refinement Id 1 Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type TFS FALCON 4i (4k x 4k) Electron Dose (electrons/Å**2) 2.4
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 2000 Maximum Defocus (nm) 5000 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version VOLUME SELECTION Dynamo IMAGE ACQUISITION FEI tomography CTF CORRECTION Gctf CTF CORRECTION RELION 4.0 MODEL FITTING ISOLDE MODEL REFINEMENT REFMAC FINAL EULER ASSIGNMENT RELION 4.0 RECONSTRUCTION RELION 4.0
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION