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hPNPase RNA loading state with extended RNA in the bottom
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-Q8TCS8-F1
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 8.408 f_angle_d 0.46 f_chiral_restr 0.044 f_bond_d 0.004 f_plane_restr 0.003
Sample Trimeric human PNPase bound to RNA in loading state with extended RNA in the bottom
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 89314 Reported Resolution (Å) 2.65 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value 77.31 Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 58.4
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 300 Maximum Defocus (nm) 2000 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 4.6.2 IMAGE ACQUISITION EPU CTF CORRECTION cryoSPARC 4.6.2 MODEL FITTING Coot 0.9.8.95 MODEL REFINEMENT PHENIX 1.21.2_5419 INITIAL EULER ASSIGNMENT cryoSPARC 4.6.2 FINAL EULER ASSIGNMENT cryoSPARC 4.7.1 CLASSIFICATION RELION 5.0 RECONSTRUCTION cryoSPARC 4.7.1
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION