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Cryo-EM structure of human TMEM87A, gluconate-bound
ELECTRON MICROSCOPY
Refinement
RMS Deviations
Key
Refinement Restraint Deviation
f_dihedral_angle_d
10.992
f_angle_d
0.475
f_chiral_restr
0.089
f_bond_d
0.002
f_plane_restr
0.002
Sample
Transmembrane protein 87A with GFP tag and Twin-strep tag with gluconate
Specimen Preparation
Sample Aggregation State
PARTICLE
Vitrification Instrument
FEI VITROBOT MARK IV
Cryogen Name
ETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
201915
Reported Resolution (Å)
3.6
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Non-uniform refinement and CTF refinement were used to improve the particle alignment and map quality.
Refinement Type
Symmetry Type
POINT
Point Symmetry
C1
Map-Model Fitting and Refinement
Id
1
Refinement Space
REAL
Refinement Protocol
RIGID BODY FIT
Refinement Target
Overall B Value
40
Fitting Procedure
Details
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 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 Type
GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)
68.15
Imaging Experiment
1
Date of Experiment
Temperature (Kelvin)
Microscope Model
FEI TITAN KRIOS
Minimum Defocus (nm)
800
Maximum Defocus (nm)
1900
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
2.7
Imaging Mode
BRIGHT FIELD
Specimen Holder Model
FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification
105000
Calibrated Magnification
58900
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
300
Imaging Details
Using Zemlin tableau in sherpa
EM Software
Task
Software Package
Version
PARTICLE SELECTION
cryoSPARC
3.3.2
IMAGE ACQUISITION
EPU
2.13
CTF CORRECTION
cryoSPARC
3.3.2
MODEL FITTING
UCSF Chimera
1.16
MODEL REFINEMENT
PHENIX
1.19.2
INITIAL EULER ASSIGNMENT
cryoSPARC
3.3.2
FINAL EULER ASSIGNMENT
cryoSPARC
3.3.2
CLASSIFICATION
cryoSPARC
3.3.2
RECONSTRUCTION
cryoSPARC
3.3.2
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION
PatchCTF in Cryosparc was used
6035205
The previous model was used as a template for particle picking. 2D class average images were generated as templates for subsequent reference-based auto-picking.