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L-cluster free apo-NifEN expressed in E. coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-C1DH03-F1-model_v4 in silico model AlphaFold AF-C1DH04-F1-model_v4
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 10.616 f_angle_d 0.541 f_chiral_restr 0.04 f_plane_restr 0.005 f_bond_d 0.002
Sample NifEN Sample Components NifE NifN
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details Plunged inside an anaerobic chamber
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 126644 Reported Resolution (Å) 3.72 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 Refinement Space Refinement Protocol Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type TFS FALCON 4i (4k x 4k) Electron Dose (electrons/Å**2) 60
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 1000 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 4.2.1 IMAGE ACQUISITION SerialEM CTF CORRECTION cryoSPARC 4.2.1 MODEL FITTING UCSF ChimeraX INITIAL EULER ASSIGNMENT cryoSPARC 4.2.1 FINAL EULER ASSIGNMENT cryoSPARC 4.2.1 RECONSTRUCTION cryoSPARC 4.2.1 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