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hPNPase bound to PO4 in loop conformation 1
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 6.071 f_angle_d 0.475 f_chiral_restr 0.044 f_bond_d 0.004 f_plane_restr 0.004
Sample Trimeric human PNPase bound to PO4 in loop conformation 1
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 187547 Reported Resolution (Å) 2.36 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 72.99 Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 45.98
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 200 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 4.62 IMAGE ACQUISITION EPU CTF CORRECTION cryoSPARC 4.62 MODEL FITTING Coot 0.9.8.95 INITIAL EULER ASSIGNMENT cryoSPARC 4.62 FINAL EULER ASSIGNMENT cryoSPARC 4.62 CLASSIFICATION cryoSPARC 4.62 RECONSTRUCTION cryoSPARC 4.62 MODEL REFINEMENT PHENIX 1.21.2_5419
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION