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CryoEM structure of class Ib Ribonucleotide reductase from Mycobacterium thermoresistibile, conformer D
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BQ1 experimental model PDB 1UZR
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.891 f_angle_d 0.604 f_chiral_restr 0.044 f_plane_restr 0.004 f_bond_d 0.002
Sample Binary complex of RNR
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 112390 Reported Resolution (Å) 3.8 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (2Bq1, 1UZR) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K2 QUANTUM (4k x 4k) Electron Dose (electrons/Å**2) 47.36
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 1500 Maximum Defocus (nm) 3500 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 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC v3.3.2 IMAGE ACQUISITION EPU CTF CORRECTION cryoSPARC v3.3.2 INITIAL EULER ASSIGNMENT cryoSPARC v3.3.2 FINAL EULER ASSIGNMENT cryoSPARC v3.3.2 CLASSIFICATION cryoSPARC v3.3.2 RECONSTRUCTION cryoSPARC v3.3.2 MODEL REFINEMENT PHENIX 1.20.1_4487
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 300000