8P2Z

Structure of human SIT1 bound to L-pipecolate (focussed map / refinement)


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6M18 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d4.122
f_angle_d0.545
f_chiral_restr0.04
f_plane_restr0.006
f_bond_d0.003
Sample
SIT1:ACE2 complex
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Detailsgrid blotted for 4sec after a 20sec wait time
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles344606
Reported Resolution (Å)3.5
Resolution MethodFSC 0.143 CUT-OFF
Other DetailscryoSPARC masked local refinement focussed on SIT1 with symmetry expanded particles after 3D classification in RELION
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1 (6M18)
Refinement SpaceREAL
Refinement ProtocolOTHER
Refinement Target
Overall B Value112
Fitting Procedure
DetailsInitial model fitting was peformed in Chimera and model building in COOT
Data Acquisition
Detector TypeGATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)50
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)1200
Maximum Defocus (nm)2400
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification105000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARC3.3.1
IMAGE ACQUISITIONEPU
CTF CORRECTIONcryoSPARC3.3.1
MODEL FITTINGCoot0.9.6
INITIAL EULER ASSIGNMENTcryoSPARC3.3.1
FINAL EULER ASSIGNMENTcryoSPARC3.3.1
CLASSIFICATIONRELION3.1.3
RECONSTRUCTIONcryoSPARC3.3.1
MODEL REFINEMENTPHENIX1.20_4459
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION808912particles from template and TOPAZ trained picking after initial 2D classification to remove junk