6B3Q

Cryo-EM structure of human insulin degrading enzyme in complex with insulin


ELECTRON MICROSCOPY

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d9.021
f_angle_d1.041
f_chiral_restr0.059
f_plane_restr0.008
f_bond_d0.005
Sample
Insulin degrading enzyme/Insulin
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentHOMEMADE PLUNGER
Cryogen NameETHANE
Sample Vitrification DetailsThe cryo grids were made using Spotiton and homemade plunger
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles116122
Reported Resolution (Å)3.7
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1
Refinement SpaceREAL
Refinement ProtocolFLEXIBLE FIT
Refinement Target
Overall B Value92
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)71.4
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)940
Maximum Defocus (nm)2200
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification22500
Calibrated Magnification46598
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONDoG Picker
IMAGE ACQUISITIONLeginon3.3
CTF CORRECTIONGctfGctf-v0.50_sm_30_cu7.5_x86_64
MODEL FITTINGCootCoot 0.8.9_pre
MODEL FITTINGUCSF ChimeraChimera 1.11.2
INITIAL EULER ASSIGNMENTRELION2.0
FINAL EULER ASSIGNMENTRELION2.0
CLASSIFICATIONRELION2.0
RECONSTRUCTIONRELION2.1
MODEL REFINEMENTPHENIXPhenix-1.12-2829
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION762283