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HSV-1 DNA polymerase beta-hairpin loop
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7LUF
Refinement RMS Deviations Key Refinement Restraint Deviation r_lrange_it 22.354 r_lrange_other 22.353 r_dihedral_angle_6_deg 16.382 r_dihedral_angle_3_deg 13.117 r_scangle_it 10.467 r_scangle_other 10.466 r_mcangle_it 9.358 r_mcangle_other 9.357 r_dihedral_angle_1_deg 7.276 r_dihedral_angle_2_deg 6.909
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 22.354 r_lrange_other 22.353 r_dihedral_angle_6_deg 16.382 r_dihedral_angle_3_deg 13.117 r_scangle_it 10.467 r_scangle_other 10.466 r_mcangle_it 9.358 r_mcangle_other 9.357 r_dihedral_angle_1_deg 7.276 r_dihedral_angle_2_deg 6.909 r_scbond_it 6.074 r_scbond_other 6.074 r_mcbond_it 5.565 r_mcbond_other 5.565 r_angle_refined_deg 1.516 r_angle_other_deg 0.475 r_nbd_refined 0.204 r_symmetry_nbd_other 0.185 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.138 r_chiral_restr 0.084 r_symmetry_nbtor_other 0.075 r_chiral_restr_other 0.01 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.001 r_bond_other_d
Sample HSV-1 DNA polymerase focused on beta-hairpin loop
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE-PROPANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 41759 Reported Resolution (Å) 2.46 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (7LUF) Refinement Space Refinement Protocol Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 58
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 500 Maximum Defocus (nm) 1500 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 165000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 3.3 IMAGE ACQUISITION EPU CTF CORRECTION CTFFIND 4.1 MODEL FITTING UCSF ChimeraX MODEL REFINEMENT Coot INITIAL EULER ASSIGNMENT cryoSPARC 3.3 FINAL EULER ASSIGNMENT cryoSPARC 4 RECONSTRUCTION cryoSPARC 4
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details NONE