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Amyloid-beta 40 type 1 filament from the leptomeninges of individual with Alzheimer's disease and cerebral amyloid angiopathy
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7Q4B
Refinement RMS Deviations Key Refinement Restraint Deviation r_long_range_B_other 19.022 r_long_range_B_refined 19.003 r_scangle_other 13.956 r_dihedral_angle_3_deg 10.485 r_mcangle_other 9.91 r_mcangle_it 9.873 r_scbond_it 8.187 r_scbond_other 8.161 r_dihedral_angle_1_deg 6.267 r_dihedral_angle_2_deg 6.162
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_other 19.022 r_long_range_B_refined 19.003 r_scangle_other 13.956 r_dihedral_angle_3_deg 10.485 r_mcangle_other 9.91 r_mcangle_it 9.873 r_scbond_it 8.187 r_scbond_other 8.161 r_dihedral_angle_1_deg 6.267 r_dihedral_angle_2_deg 6.162 r_mcbond_it 6.072 r_mcbond_other 6.04 r_angle_refined_deg 1.335 r_angle_other_deg 0.634 r_chiral_restr 0.06 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.003 r_bond_other_d 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Sample Amyloid-beta 40 doublet filament extracted from the human brain with Alzheimer's disease and cerebral amyloid angiopathy
Specimen Preparation Sample Aggregation State FILAMENT Vitrification Instrument Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method HELICAL Number of Particles 32218 Reported Resolution (Å) 2.7 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type HELICAL Axial Symmetry C1 Axial Rise 2.44 Angular Rotation -179.53
Map-Model Fitting and Refinement Id 1 (7Q4B) Refinement Space Refinement Protocol 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 FEI TITAN KRIOS Minimum Defocus (nm) 1000 Maximum Defocus (nm) 2400 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 RELION 4.0 IMAGE ACQUISITION EPU CTF CORRECTION RELION MODEL FITTING Coot MODEL REFINEMENT REFMAC INITIAL EULER ASSIGNMENT RELION FINAL EULER ASSIGNMENT RELION CLASSIFICATION RELION RECONSTRUCTION RELION
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION