29KM | pdb_000029km

Cryo-EM structure of Bacillus subtilis DnaB

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	11.383
f_angle_d	0.404
f_chiral_restr	0.036
f_plane_restr	0.003
f_bond_d	0.002

Sample
Bacillus subtilis DnaB

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	LEICA EM GP
Cryogen Name	ETHANE
Sample Vitrification Details	Leica EM GP2

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	144168
Reported Resolution (Å)	3.1
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C2

Map-Model Fitting and Refinement
Id	1
Refinement Space	REAL
Refinement Protocol	RIGID BODY FIT
Refinement Target
Overall B Value	139.5
Fitting Procedure
Details	Initial rigid body fitting was done using Chimera X (Fit to Map). After retracing terminal residues, as well as rebuilding around Arg57, further modelling and real space refinement was used to refine the final model.

Data Acquisition
Detector Type	GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)	40

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	TFS KRIOS
Minimum Defocus (nm)	700
Maximum Defocus (nm)	3000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cryoSPARC	4.7.1
IMAGE ACQUISITION	EPU
CTF CORRECTION	cryoSPARC	4.7.1
MODEL FITTING	UCSF ChimeraX	10.0
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	PHENIX	1.21.2_5419

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		2578235