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Dimer of ATPase BrxC containing a Walker B mutation and bound to ATP from the Acinetobacter BREX system
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
9.21
f_angle_d
0.518
f_chiral_restr
0.039
f_bond_d
0.004
f_plane_restr
0.003
Sample
BrxC Walker B
Specimen Preparation
Sample Aggregation State
3D ARRAY
Vitrification Instrument
FEI VITROBOT MARK IV
Cryogen Name
ETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
477102
Reported Resolution (Å)
2.95
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
FLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector Type
GATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)
50
Imaging Experiment
1
Date of Experiment
Temperature (Kelvin)
Microscope Model
TFS GLACIOS
Minimum Defocus (nm)
800
Maximum Defocus (nm)
2000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
2.7
Imaging Mode
BRIGHT FIELD
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
200
Imaging Details
EM Software
Task
Software Package
Version
PARTICLE SELECTION
cryoSPARC
4.5.3
PARTICLE SELECTION
cryoSPARC
4.5.3
CTF CORRECTION
cryoSPARC
4.5.3
MODEL FITTING
ISOLDE
MODEL FITTING
Coot
0.9.8.93
MODEL FITTING
Coot
1.1.18
INITIAL EULER ASSIGNMENT
cryoSPARC
4.5.3
INITIAL EULER ASSIGNMENT
cryoSPARC
4.5.3
FINAL EULER ASSIGNMENT
cryoSPARC
4.5.3
RECONSTRUCTION
cryoSPARC
4.5.3
MODEL REFINEMENT
PHENIX
1.21.1_5286
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION
3132271
Blob picking on a 200 micrograph resulted in 112,543 particles, which were rigorously sorted/classified and used to generate templates for template picking on the full dataset