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The H/ACA RNP lobe of human telomerase with the dyskerin thumb loop in an open 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 36.863 r_dihedral_angle_4_deg 18.673 r_long_range_B_refined 14.361 r_long_range_B_other 14.36 r_dihedral_angle_3_deg 12.529 r_dihedral_angle_1_deg 7.514 r_mcangle_it 7.494 r_mcangle_other 7.493 r_scangle_other 7.35 r_mcbond_it 4.511
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.863 r_dihedral_angle_4_deg 18.673 r_long_range_B_refined 14.361 r_long_range_B_other 14.36 r_dihedral_angle_3_deg 12.529 r_dihedral_angle_1_deg 7.514 r_mcangle_it 7.494 r_mcangle_other 7.493 r_scangle_other 7.35 r_mcbond_it 4.511 r_mcbond_other 4.511 r_scbond_it 4.335 r_scbond_other 4.335 r_angle_refined_deg 1.092 r_angle_other_deg 0.937 r_chiral_restr 0.061 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 145627 Reported Resolution (Å) 3.1 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 ISOLDE 1.5 MODEL FITTING UCSF ChimeraX 1.5 INITIAL EULER ASSIGNMENT RELION 4 FINAL EULER ASSIGNMENT RELION 4 CLASSIFICATION RELION 4 RECONSTRUCTION RELION 4 MODEL REFINEMENT REFMAC 5.8 MODEL REFINEMENT PHENIX 1.20-4459
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 18744992