8HTT

Cryo-EM structure of human TMEM87A, gluconate-bound


ELECTRON MICROSCOPY

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d10.992
f_angle_d0.475
f_chiral_restr0.089
f_bond_d0.002
f_plane_restr0.002
Sample
Transmembrane protein 87A with GFP tag and Twin-strep tag with gluconate
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles201915
Reported Resolution (Å)3.6
Resolution MethodFSC 0.143 CUT-OFF
Other DetailsNon-uniform refinement and CTF refinement were used to improve the particle alignment and map quality.
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement Target
Overall B Value40
Fitting Procedure
DetailsChimera Fit in map tool was used for initial local fitting. Then, Real-space refinement with the rigid body option in PHENIX was used for flexible fit ...Chimera Fit in map tool was used for initial local fitting. Then, Real-space refinement with the rigid body option in PHENIX was used for flexible fitting.
Data Acquisition
Detector TypeGATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)68.15
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)800
Maximum Defocus (nm)1900
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification105000
Calibrated Magnification58900
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging DetailsUsing Zemlin tableau in sherpa
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARC3.3.2
IMAGE ACQUISITIONEPU2.13
CTF CORRECTIONcryoSPARC3.3.2
MODEL FITTINGUCSF Chimera1.16
MODEL REFINEMENTPHENIX1.19.2
INITIAL EULER ASSIGNMENTcryoSPARC3.3.2
FINAL EULER ASSIGNMENTcryoSPARC3.3.2
CLASSIFICATIONcryoSPARC3.3.2
RECONSTRUCTIONcryoSPARC3.3.2
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTIONPatchCTF in Cryosparc was used6035205The previous model was used as a template for particle picking. 2D class average images were generated as templates for subsequent reference-based auto-picking.