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The H/ACA RNP lobe of human telomerase with the dyskerin thumb loop in a semi-closed conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7BGB
Refinement RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.817 r_long_range_B_refined 15.21 r_long_range_B_other 15.21 r_dihedral_angle_4_deg 14.154 r_dihedral_angle_3_deg 11.836 r_scangle_other 8.232 r_mcangle_it 7.52 r_mcangle_other 7.519 r_dihedral_angle_1_deg 5.743 r_scbond_it 4.958
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.817 r_long_range_B_refined 15.21 r_long_range_B_other 15.21 r_dihedral_angle_4_deg 14.154 r_dihedral_angle_3_deg 11.836 r_scangle_other 8.232 r_mcangle_it 7.52 r_mcangle_other 7.519 r_dihedral_angle_1_deg 5.743 r_scbond_it 4.958 r_scbond_other 4.958 r_mcbond_it 4.705 r_mcbond_other 4.705 r_angle_refined_deg 1.077 r_angle_other_deg 0.923 r_chiral_restr 0.065 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 telomerase H/ACA RNP lobe Sample Components Telomerase H/ACA RNP lobe Human telomerase RNA
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 199360 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 (7BGB) Refinement Space Refinement Protocol Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 48
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1000 Maximum Defocus (nm) 3000 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 81000 Calibrated Magnification 45872 Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION RELION 4 IMAGE ACQUISITION EPU 2.13.0.3175REL CTF CORRECTION CTFFIND 4 MODEL FITTING Coot 0.9.8.1 MODEL FITTING UCSF ChimeraX 1.5 MODEL FITTING ISOLDE 1.5 INITIAL EULER ASSIGNMENT RELION 4 FINAL EULER ASSIGNMENT RELION 4 CLASSIFICATION RELION 4 RECONSTRUCTION RELION 4 MODEL REFINEMENT REFMAC 5.8
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 18744992