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 7Q4D | pdb_00007q4d

Local refinement structure of the two interacting N-domains of full-length, dimeric, soluble somatic angiotensin I-converting enzyme


ELECTRON MICROSCOPY

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d13.2209
f_angle_d0.8684
f_chiral_restr0.0469
f_plane_restr0.0136
f_bond_d0.0069
Sample
Full-length, soluble, dimeric somatic angiotensin I-converting enzyme
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification DetailsDiluted protein (in buffer containing zinc chloride and sodium chloride) was incubated on ice for 30 minutes after which it was applied to the grid, i ...Diluted protein (in buffer containing zinc chloride and sodium chloride) was incubated on ice for 30 minutes after which it was applied to the grid, incubated for 30 seconds, and blotted for 3 seconds before plunging
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles215632
Reported Resolution (Å)3.78
Resolution MethodFSC 0.143 CUT-OFF
Other DetailsLocal refinement (C1) with a mask around the two interacting N-domains following C-domain particle subtraction in RELION and C2 symmetry expansion in ...Local refinement (C1) with a mask around the two interacting N-domains following C-domain particle subtraction in RELION and C2 symmetry expansion in cryoSPARC
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1
Refinement SpaceREAL
Refinement ProtocolFLEXIBLE FIT
Refinement TargetCorrelation coefficient
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)43
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)1800
Maximum Defocus (nm)3000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification81000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONTopaz0.2.5
IMAGE ACQUISITIONEPU
CTF CORRECTIONcryoSPARC3.2
MODEL FITTINGISOLDE1.2.0
MODEL REFINEMENTPHENIX1.19.2
INITIAL EULER ASSIGNMENTcryoSPARC3.2
FINAL EULER ASSIGNMENTcryoSPARC3.2
CLASSIFICATIONcryoSPARC3.2
RECONSTRUCTIONcryoSPARC3.2
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTIONcryoSPARC patch-based CTF estimation1727045Topaz-denoising was performed on all curated micrographs, a Topaz model trained on this dataset, and used for picking