8KB4

Cryo-EM structure of human TMEM87A A308M

ELECTRON MICROSCOPY

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	11.87
f_angle_d	0.443
f_chiral_restr	0.036
f_bond_d	0.004
f_plane_restr	0.003

Sample
Transmembrane protein 87A A308M with GFP tag and Twin-strep tag

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	360876
Reported Resolution (Å)	3.1
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT

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)	67.7

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	4.2.1
IMAGE ACQUISITION	EPU	2.13
CTF CORRECTION	cryoSPARC	4.2.1
MODEL FITTING	UCSF Chimera	1.16
MODEL REFINEMENT	PHENIX	1.19.2
INITIAL EULER ASSIGNMENT	cryoSPARC	4.2.1
FINAL EULER ASSIGNMENT	cryoSPARC	4.2.1
CLASSIFICATION	cryoSPARC	4.2.1
RECONSTRUCTION	cryoSPARC	4.2.1

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	8101104	96,330 particles were first picked using a blob picker of cryoSPARC. 2D class average images were generated as templates for subsequent reference-based auto-picking.

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.