8OQY

Structure of apo form of human gamma-secretase PSEN1 APH-1B isoform reconstituted into lipid nanodisc


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5FN5 
in silico modelModeller 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d15.175
f_angle_d0.941
f_chiral_restr0.058
f_bond_d0.006
f_plane_restr0.006
Sample
Gamma secretase
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentGATAN CRYOPLUNGE 3
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles111197
Reported Resolution (Å)3.3
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1 (5FN5)
Refinement SpaceREAL
Refinement ProtocolFLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)61
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelJEOL CRYO ARM 300
Minimum Defocus (nm)1200
Maximum Defocus (nm)2000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.55
Imaging ModeBRIGHT FIELD
Specimen Holder ModelJEOL CRYOSPECPORTER
Nominal Magnification60000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcrYOLO1.7
IMAGE ACQUISITIONSerialEM3.8.2
CTF CORRECTIONCTFFIND4.1.14
MODEL FITTINGCoot0.9.8
MODEL REFINEMENTPHENIX1.19.2
INITIAL EULER ASSIGNMENTRELION3.1
FINAL EULER ASSIGNMENTRELION3.1
CLASSIFICATIONRELION3.1
RECONSTRUCTIONRELION3.1
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION986830