9OA2 | pdb_00009oa2

Ecoli DnaB helicase and Phage Lambda loader P with ADP-Mg in a 6:6 stoichiometry ratio.

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1B79
in silico model	AlphaFold
experimental model	PDB	8V9S

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	9.3107
f_angle_d	0.5785
f_chiral_restr	0.0406
f_plane_restr	0.0045
f_bond_d	0.0025

Sample
Replication initiation intermediate with Escherichia coli DnaB helicase and Phage Lambda loader P in a 6:6 stoichiometry ratio
Sample Components
Ecoli DnaB helicase
Phage Lambda loader P

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	Protein BP (1.5 uM), ssDNA (1.875 uM), and LO-156-299-NHis (2.25 uM) was mixed at 1.25 and 1.5 molar excess, respectively. 3uL of the sample was added to a plasma-cleaned grid at 4 degrees celsius, 100 percent humidity, blot force 4, blot time 4s, wait time 30s, total blots 1, and plunge-frozen into liquid nitrogen-cooled ethane.

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	572557
Reported Resolution (Å)	3.85
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (1B79, 8V9S)
Refinement Space	REAL
Refinement Protocol	OTHER
Refinement Target
Overall B Value	153.98
Fitting Procedure
Details

Data Acquisition
Detector Type	GATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)	51.19

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	TFS KRIOS
Minimum Defocus (nm)	600
Maximum Defocus (nm)	2700
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	81000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cryoSPARC	4
IMAGE ACQUISITION	Leginon
CTF CORRECTION	cryoSPARC	4
MODEL FITTING	PHENIX	1.21.2_5419
RECONSTRUCTION	cryoSPARC	4
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		2315940	Particle picking was performed using Topaz in CryoSPARC.