8UY7 | pdb_00008uy7

Magnesium transporter MgtA dimer from E. coli in 5 mM MgCl2

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	4.366
f_angle_d	0.529
f_chiral_restr	0.04
f_plane_restr	0.005
f_bond_d	0.003

Sample
Magnesium transporter MgtA from Escherichia coli in the dimeric form in the presence of 5 mM MgCl2

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	LEICA EM GP
Cryogen Name	ETHANE
Sample Vitrification Details	Quantifoil R1.2/1.3 400 copper mesh grids (EMS) were glow discharged in a PELCO easiGlow Glow Discharge Cleaning System (Ted Pella) at 15 mA for 1 min. A 3 microliter sample at a concentration of 3.2 mg/mL was applied to the glow discharged grids. After blotting for 5 s in a Leica GP-EM2 plunger (Leica Microsystems, Wetzlar, Germany) with the chamber set to 5 degrees C and 95% humidity, the grids were immediately plunge frozen into liquid ethane and stored in liquid nitrogen.

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	160139
Reported Resolution (Å)	2.93
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C2

Map-Model Fitting and Refinement
Id	1	2	3
Refinement Space	REAL	REAL	REAL
Refinement Protocol	RIGID BODY FIT	FLEXIBLE FIT	FLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)	60

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	TFS KRIOS
Minimum Defocus (nm)	1000
Maximum Defocus (nm)	2000
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	60241
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cryoSPARC
IMAGE ACQUISITION	SerialEM	3.8-11
CTF CORRECTION	cryoSPARC
MODEL FITTING	UCSF Chimera	8.6.10
MODEL FITTING	Coot	0.9.8.7
MODEL REFINEMENT	Coot	0.9.8.7
MODEL FITTING	PHENIX	1.20.1-4487
MODEL REFINEMENT	PHENIX	1.20.1-4487
INITIAL EULER ASSIGNMENT	cryoSPARC
FINAL EULER ASSIGNMENT	cryoSPARC
CLASSIFICATION	cryoSPARC
RECONSTRUCTION	cryoSPARC

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		3353940	1,578,214 particles were initially selected from dataset 1 (10,164 selected movies from 10,246 total). 1,775,726 particles were initially selected from dataset 2 (5,778 selected movies from 6,906 total).