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Cryo-EM structure of MlaFEDB in nanodiscs with phospholipid substrates
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5UW2 experimental model PDB 6CM1
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.398 f_angle_d 0.549 f_chiral_restr 0.043 f_bond_d 0.003 f_plane_restr 0.003
Sample MlaFEDB complex with two bound phospholipid substrates in MSP1D1 nanodisc
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 731205 Reported Resolution (Å) 3.05 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (5UW2, 6CM1) Refinement Space REAL Refinement Protocol OTHER Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K2 SUMMIT (4k x 4k) Electron Dose (electrons/Å**2) 71
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) Maximum Defocus (nm) 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 29000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION RELION 2.1 IMAGE ACQUISITION Leginon CTF CORRECTION Gctf 1.18 CTF CORRECTION CTFFIND 4.1.10 MODEL FITTING UCSF Chimera MODEL FITTING Coot INITIAL EULER ASSIGNMENT cryoSPARC 0.6 INITIAL EULER ASSIGNMENT RELION 3.0 INITIAL EULER ASSIGNMENT RELION 3.1 FINAL EULER ASSIGNMENT cryoSPARC 2.12 RECONSTRUCTION cryoSPARC 2.12 MODEL REFINEMENT PHENIX
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 1283606