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HK97 small terminase in complex with DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6Z6E
Refinement RMS Deviations Key Refinement Restraint Deviation r_lrange_it 35.901 r_lrange_other 35.901 r_scangle_it 22.869 r_scangle_other 22.868 r_dihedral_angle_3_deg 13.993 r_dihedral_angle_6_deg 13.981 r_mcangle_it 13.854 r_mcangle_other 13.853 r_scbond_it 13.625 r_scbond_other 13.625
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 35.901 r_lrange_other 35.901 r_scangle_it 22.869 r_scangle_other 22.868 r_dihedral_angle_3_deg 13.993 r_dihedral_angle_6_deg 13.981 r_mcangle_it 13.854 r_mcangle_other 13.853 r_scbond_it 13.625 r_scbond_other 13.625 r_mcbond_it 8.971 r_mcbond_other 8.969 r_dihedral_angle_2_deg 5.981 r_dihedral_angle_1_deg 5.856 r_paralell_plane_angle_deg 2.262 r_angle_refined_deg 1.335 r_dihedral_angle_other_2_deg 0.511 r_angle_other_deg 0.434 r_nbd_refined 0.223 r_symmetry_nbd_other 0.188 r_nbtor_refined 0.187 r_xyhbond_nbd_refined 0.17 r_chiral_restr 0.102 r_ncsr_local_group_10 0.1 r_ncsr_local_group_15 0.1 r_ncsr_local_group_32 0.099 r_ncsr_local_group_12 0.097 r_ncsr_local_group_9 0.096 r_ncsr_local_group_13 0.096 r_ncsr_local_group_1 0.094 r_ncsr_local_group_8 0.094 r_ncsr_local_group_30 0.094 r_ncsr_local_group_14 0.093 r_ncsr_local_group_11 0.092 r_ncsr_local_group_33 0.092 r_ncsr_local_group_4 0.091 r_ncsr_local_group_5 0.091 r_ncsr_local_group_21 0.09 r_ncsr_local_group_22 0.09 r_ncsr_local_group_36 0.089 r_ncsr_local_group_7 0.087 r_ncsr_local_group_28 0.087 r_ncsr_local_group_31 0.087 r_ncsr_local_group_25 0.086 r_ncsr_local_group_26 0.086 r_ncsr_local_group_27 0.084 r_ncsr_local_group_34 0.084 r_ncsr_local_group_3 0.083 r_ncsr_local_group_35 0.082 r_ncsr_local_group_6 0.081 r_ncsr_local_group_18 0.081 r_ncsr_local_group_24 0.08 r_ncsr_local_group_17 0.079 r_ncsr_local_group_2 0.078 r_ncsr_local_group_20 0.078 r_ncsr_local_group_16 0.077 r_ncsr_local_group_19 0.072 r_symmetry_nbtor_other 0.071 r_ncsr_local_group_29 0.07 r_ncsr_local_group_23 0.065 r_gen_planes_refined 0.007 r_bond_refined_d 0.006 r_gen_planes_other 0.001 r_bond_other_d
Sample HK97 small terminase in complex with DNA
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 76628 Reported Resolution (Å) 3 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (6z6e) Refinement Space RECIPROCAL Refinement Protocol AB INITIO MODEL Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K2 SUMMIT (4k x 4k) Electron Dose (electrons/Å**2) 53.6
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1000 Maximum Defocus (nm) 2400 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 130000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION Topaz IMAGE ACQUISITION EPU CTF CORRECTION CTFFIND 4.1 CTF CORRECTION RELION 3.1 MODEL FITTING Coot 0.9.8 INITIAL EULER ASSIGNMENT RELION 3.1 FINAL EULER ASSIGNMENT RELION 3.1 CLASSIFICATION RELION 3.1 RECONSTRUCTION RELION 3.1 MODEL REFINEMENT REFMAC 5.8.0411
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION CTF correction in RELION 1144385 dataset 1:306866
dataset 2:837519