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Structure of the Azotobacter vinelandii NifL-NifA complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 7.313 f_angle_d 0.564 f_chiral_restr 0.04 f_plane_restr 0.005 f_bond_d 0.002
Sample NifL-NifA complex from Azotobacter vinelandii
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 209009 Reported Resolution (Å) 6.45 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 OTHER Refinement Target cross-correlation coefficient Overall B Value 456 Fitting Procedure Details Real space refinement in COOT and PHENIX
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 50
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 700 Maximum Defocus (nm) 2200 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 4.5.3 IMAGE ACQUISITION EPU 3.5.1 CTF CORRECTION cryoSPARC 4.5.3 MODEL FITTING UCSF ChimeraX 1.9 MODEL FITTING Coot 0.9.8.95 EL INITIAL EULER ASSIGNMENT cryoSPARC 4.5.3 FINAL EULER ASSIGNMENT cryoSPARC 4.5.3 CLASSIFICATION cryoSPARC 4.5.3 RECONSTRUCTION cryoSPARC 4.5.3 MODEL REFINEMENT PHENIX 1.21_5207
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 2186245 Used template-based picking with 2D-classes from blob picker