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C1 turret to capsid interface of full Haloferax tailed virus 1 adjacent to the portal-capsid interface.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model
Refinement RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.437 r_dihedral_angle_4_deg 20.456 r_dihedral_angle_3_deg 12.785 r_lrange_it 11.367 r_dihedral_angle_1_deg 8.264 r_scangle_it 6.435 r_mcangle_it 4.545 r_scbond_it 3.972 r_mcbond_it 2.739 r_angle_refined_deg 1.619
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.437 r_dihedral_angle_4_deg 20.456 r_dihedral_angle_3_deg 12.785 r_lrange_it 11.367 r_dihedral_angle_1_deg 8.264 r_scangle_it 6.435 r_mcangle_it 4.545 r_scbond_it 3.972 r_mcbond_it 2.739 r_angle_refined_deg 1.619 r_nbtor_refined 0.29 r_nbd_refined 0.197 r_ncsr_local_group_30 0.145 r_ncsr_local_group_20 0.144 r_ncsr_local_group_19 0.141 r_ncsr_local_group_24 0.14 r_ncsr_local_group_21 0.139 r_ncsr_local_group_28 0.138 r_ncsr_local_group_23 0.137 r_ncsr_local_group_29 0.136 r_ncsr_local_group_22 0.133 r_ncsr_local_group_26 0.124 r_ncsr_local_group_27 0.123 r_metal_ion_refined 0.119 r_ncsr_local_group_33 0.118 r_ncsr_local_group_25 0.116 r_ncsr_local_group_31 0.114 r_ncsr_local_group_32 0.114 r_chiral_restr 0.113 r_ncsr_local_group_1 0.093 r_ncsr_local_group_2 0.093 r_ncsr_local_group_17 0.087 r_ncsr_local_group_18 0.087 r_xyhbond_nbd_refined 0.086 r_ncsr_local_group_7 0.086 r_ncsr_local_group_14 0.083 r_ncsr_local_group_5 0.07 r_ncsr_local_group_3 0.068 r_ncsr_local_group_11 0.068 r_ncsr_local_group_16 0.068 r_ncsr_local_group_15 0.066 r_ncsr_local_group_12 0.065 r_ncsr_local_group_10 0.063 r_ncsr_local_group_8 0.061 r_ncsr_local_group_13 0.044 r_ncsr_local_group_9 0.043 r_ncsr_local_group_4 0.039 r_ncsr_local_group_6 0.039 r_gen_planes_refined 0.011 r_bond_refined_d 0.007
Sample Haloferax tailed virus 1
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 102012 Reported Resolution (Å) 2.7 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 Refinement Space RECIPROCAL Refinement Protocol AB INITIO MODEL Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type TFS FALCON 4i (4k x 4k) Electron Dose (electrons/Å**2) 54.6
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 800 Maximum Defocus (nm) 2000 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version IMAGE ACQUISITION EPU 5 CTF CORRECTION RELION 4.0-beta MODEL FITTING Coot MODEL FITTING UCSF ChimeraX MODEL FITTING ISOLDE MODEL REFINEMENT REFMAC
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION