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The Human LINE-1 ORF2p target-primed reverse transcription complex with the fingers domain in a closed conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Refinement RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 11.736 r_long_range_B_other 11.736 r_dihedral_angle_3_deg 11.644 r_dihedral_angle_1_deg 8.895 r_scangle_other 7.411 r_mcangle_it 6.583 r_mcangle_other 6.583 r_dihedral_angle_2_deg 5.403 r_scbond_it 4.624 r_scbond_other 4.624
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 11.736 r_long_range_B_other 11.736 r_dihedral_angle_3_deg 11.644 r_dihedral_angle_1_deg 8.895 r_scangle_other 7.411 r_mcangle_it 6.583 r_mcangle_other 6.583 r_dihedral_angle_2_deg 5.403 r_scbond_it 4.624 r_scbond_other 4.624 r_mcbond_other 4.035 r_mcbond_it 4.034 r_angle_refined_deg 1.531 r_angle_other_deg 0.669 r_chiral_restr 0.109 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Sample Human LINE-1 ORF2p target-primed reverse transcription complex with the fingers domain in a closed conformation Sample Components ORF2p Target 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 185228 Reported Resolution (Å) 2.5 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 Refinement Space Refinement Protocol Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type TFS FALCON 4i (4k x 4k) Electron Dose (electrons/Å**2) 60
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 8000 Maximum Defocus (nm) 22000 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 PARTICLE SELECTION RELION 5 IMAGE ACQUISITION EPU CTF CORRECTION CTFFIND 4.1 MODEL FITTING Coot 0.9.8.92 MODEL FITTING ISOLDE 1.8 MODEL FITTING UCSF ChimeraX 1.8 MODEL REFINEMENT PHENIX 1.21.1-5286 MODEL REFINEMENT Servalcat 0.4.72 INITIAL EULER ASSIGNMENT RELION 5 FINAL EULER ASSIGNMENT RELION 5 CLASSIFICATION RELION 5 RECONSTRUCTION RELION 5
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 4568277