8QN7

Amyloid-beta 40 type 1 filament from the leptomeninges of individual with Alzheimer's disease and cerebral amyloid angiopathy


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7Q4B 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_other19.022
r_long_range_B_refined19.003
r_scangle_other13.956
r_dihedral_angle_3_deg10.485
r_mcangle_other9.91
r_mcangle_it9.873
r_scbond_it8.187
r_scbond_other8.161
r_dihedral_angle_1_deg6.267
r_dihedral_angle_2_deg6.162
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_other19.022
r_long_range_B_refined19.003
r_scangle_other13.956
r_dihedral_angle_3_deg10.485
r_mcangle_other9.91
r_mcangle_it9.873
r_scbond_it8.187
r_scbond_other8.161
r_dihedral_angle_1_deg6.267
r_dihedral_angle_2_deg6.162
r_mcbond_it6.072
r_mcbond_other6.04
r_angle_refined_deg1.335
r_angle_other_deg0.634
r_chiral_restr0.06
r_bond_refined_d0.006
r_gen_planes_refined0.006
r_gen_planes_other0.003
r_bond_other_d0.001
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 StateFILAMENT
Vitrification Instrument
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodHELICAL
Number of Particles32218
Reported Resolution (Å)2.7
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypeHELICAL
Axial SymmetryC1
Axial Rise2.44
Angular Rotation-179.53
Map-Model Fitting and Refinement
Id1 (7Q4B)
Refinement Space
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeFEI FALCON IV (4k x 4k)
Electron Dose (electrons/Å**2)40
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)1000
Maximum Defocus (nm)2400
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONRELION4.0
IMAGE ACQUISITIONEPU
CTF CORRECTIONRELION
MODEL FITTINGCoot
MODEL REFINEMENTREFMAC
INITIAL EULER ASSIGNMENTRELION
FINAL EULER ASSIGNMENTRELION
CLASSIFICATIONRELION
RECONSTRUCTIONRELION
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION