7YOO

Complex structure of Neuropeptide Y Y2 receptor in complex with NPY and Gi


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7DDZ 
experimental modelPDB 7VGX 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d13.321
f_angle_d0.431
f_chiral_restr0.039
f_plane_restr0.003
f_bond_d0.002
Sample
Complex structure of NPY-Y2R-Gi-scFv16
Sample Components
Guanine nucleotide-binding protein
scFv16
NPY
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles500366
Reported Resolution (Å)3.11
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1 (7DDZ, 7VGX, 7VGX, 7VGX, 7VGX)
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)66
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)1000
Maximum Defocus (nm)2250
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 SELECTIONcryoSPARC3.2
CTF CORRECTIONcryoSPARC3.2
MODEL FITTINGPHENIX1.19.2-4158
MODEL REFINEMENTPHENIX1.19.2-4158
INITIAL EULER ASSIGNMENTcryoSPARC3.2
FINAL EULER ASSIGNMENTcryoSPARC3.2
RECONSTRUCTIONcryoSPARC3.2
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION9842630