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Magnesium transporter MgtA dimer from E. coli in 5 mM MgCl2 and 5 mM ADP
ELECTRON MICROSCOPY
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
3.67
f_angle_d
0.455
f_chiral_restr
0.039
f_plane_restr
0.004
f_bond_d
0.002
Sample
Magnesium transporter MgtA from Escherichia coli in the dimeric form in the presence of 5 mM MgCl2 and 5 mM ADP
Specimen Preparation
Sample Aggregation State
PARTICLE
Vitrification Instrument
LEICA EM GP
Cryogen Name
ETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
28666
Reported Resolution (Å)
3.75
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type
POINT
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)
50
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
1456447
302,981 particles were initially selected from dataset 1 (1,897 selected movies from 2,519 total).
1,153,466 particles were initially selected from dataset 2 (7,082 selected movies from 7,107 total).