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Structure of apo form of human gamma-secretase PSEN1 APH-1B isoform reconstituted into lipid nanodisc
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5FN5 in silico model Modeller
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.175 f_angle_d 0.941 f_chiral_restr 0.058 f_bond_d 0.006 f_plane_restr 0.006
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument GATAN CRYOPLUNGE 3 Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 111197 Reported Resolution (Å) 3.3 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (5FN5) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 61
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model JEOL CRYO ARM 300 Minimum Defocus (nm) 1200 Maximum Defocus (nm) 2000 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.55 Imaging Mode BRIGHT FIELD Specimen Holder Model JEOL CRYOSPECPORTER Nominal Magnification 60000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION crYOLO 1.7 IMAGE ACQUISITION SerialEM 3.8.2 CTF CORRECTION CTFFIND 4.1.14 MODEL FITTING Coot 0.9.8 MODEL REFINEMENT PHENIX 1.19.2 INITIAL EULER ASSIGNMENT RELION 3.1 FINAL EULER ASSIGNMENT RELION 3.1 CLASSIFICATION RELION 3.1 RECONSTRUCTION RELION 3.1
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 986830