☰ Navigation Tabs
The Structure of ApoB100 from Human Low-Density Lipoprotein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Sample apolipoprotein B-100
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 52843 Reported Resolution (Å) 9 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 FLEXIBLE FIT Refinement Target cross-correlation coefficient Overall B Value Fitting Procedure Details The Molecular Dynamics Flexible Fitting protocol was applied using NAMD 3.0
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) 800 Maximum Defocus (nm) 2800 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 4 IMAGE ACQUISITION SerialEM CTF CORRECTION cryoSPARC 4 MODEL FITTING NAMD 3.0 INITIAL EULER ASSIGNMENT cryoSPARC 4 FINAL EULER ASSIGNMENT cryoSPARC 4 CLASSIFICATION cryoSPARC 4 RECONSTRUCTION cryoSPARC 4 MODEL REFINEMENT UCSF ChimeraX 1.6.1 MODEL REFINEMENT PHENIX 1.2.0
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 600000