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Cryo-EM structure of LptDE-YedD complex from Escherichia Coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Sample LPS-assembly complex LptDE with lipoprotein YedD
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument GATAN CRYOPLUNGE 3 Cryogen Name ETHANE Sample Vitrification Details Blot 3-4 seconds
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 56171 Reported Resolution (Å) 3.57 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 Overall B Value 78.86 Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 60
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model JEOL CRYO ARM 300 Minimum Defocus (nm) 800 Maximum Defocus (nm) 2000 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.55 Imaging Mode BRIGHT FIELD Specimen Holder Model JEOL CRYOSPECPORTER Nominal Magnification Calibrated Magnification 60000 Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION crYOLO 1.8.4 CTF CORRECTION RELION 3.1 CTF CORRECTION MotionCorr2 1.3 CTF CORRECTION CTFFIND 4 CTF CORRECTION PHENIX CTF CORRECTION Coot 0.8.9 CTF CORRECTION UCSF Chimera 1.15 CTF CORRECTION PyMOL 2.2 CTF CORRECTION SerialEM CTF CORRECTION cryoSPARC MODEL FITTING Coot 0.8.9 RECONSTRUCTION cryoSPARC 4.4.1 MODEL REFINEMENT PHENIX
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details NONE