☰ Navigation Tabs
Cryo-EM structure of renal amyloid fibril from a variant apolipoprotein A-I R173P amyloidosis patient
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9PVY
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 5.141 f_angle_d 0.586 f_chiral_restr 0.043 f_bond_d 0.003 f_plane_restr 0.003
Sample amyloid fibrils of apoliprotein A-I amyloidosis, variant R173P from renal tissue
Specimen Preparation Sample Aggregation State FILAMENT Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method HELICAL Number of Particles 133438 Reported Resolution (Å) 2.73 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type HELICAL Axial Symmetry C1 Axial Rise 4.85 Angular Rotation -0.67
Map-Model Fitting and Refinement Id 1 (9PVY) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type FEI FALCON IV (4k x 4k) Electron Dose (electrons/Å**2) 40
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 800 Maximum Defocus (nm) 2600 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION Topaz IMAGE ACQUISITION EPU CTF CORRECTION CTFFIND MODEL FITTING Coot 0.9 MODEL REFINEMENT PHENIX 1.20.1_4487 INITIAL EULER ASSIGNMENT RELION 4.0 FINAL EULER ASSIGNMENT RELION 4.0 CLASSIFICATION RELION 4.0 RECONSTRUCTION RELION 4.0
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details NONE RELION 4 built in CTFFIND