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Cryo-EM structure of the dimeric form of the anaerobic ribonucleotide reductase from Prevotella copri produced in the presence of dATP and CTP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8P2C
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.077 f_angle_d 0.48 f_chiral_restr 0.042 f_plane_restr 0.003 f_bond_d 0.002
Sample Anaerobic ribonucleotide reductase from Prevotella copri produced in the presence of dATP and CTP
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details blot force 1, 5s blot time
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 1132695 Reported Resolution (Å) 2.59 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (8P2C) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target correlation coefficient Overall B Value 45 Fitting Procedure Details Manual fitting was done using Coot and automatic real space refinement used phenix.refine
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 38
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 600 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 105000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 3.2.0 IMAGE ACQUISITION EPU 2.8.1 CTF CORRECTION cryoSPARC 3.2.0 MODEL FITTING Coot 0.9.8.7 MODEL REFINEMENT PHENIX 1.19.2-4158 INITIAL EULER ASSIGNMENT cryoSPARC 3.3.2 FINAL EULER ASSIGNMENT cryoSPARC 4.1.2 CLASSIFICATION cryoSPARC 4.1.2 RECONSTRUCTION cryoSPARC 4.1.2
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION Patch CTF correction in cryoSPARC 5762760