Experiment: 9Y7H

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3OHM
experimental model	PDB	1GG2

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	11.31
f_angle_d	0.465
f_chiral_restr	0.039
f_plane_restr	0.004
f_bond_d	0.003

Sample
Crosslinked complex of Gb1g2 and PLCb3

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	92777
Reported Resolution (Å)	4.4
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT

Map-Model Fitting and Refinement
Id	1 (4GNK, 1gp2)
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details	Crystal structures of Gbetagamma and PLCbeta3 (PDB IDs 1GP2 and 4GNK) were rigid-body fit into the cryo-EM map using Chimera (58). The model was then ...	Crystal structures of Gbetagamma and PLCbeta3 (PDB IDs 1GP2 and 4GNK) were rigid-body fit into the cryo-EM map using Chimera (58). The model was then refined using molecular dynamic flexible fitting (MDFF)(48). MDFF configuration files were generated using VMD. During MDFF simulation, Gbetagamma was set as rigid with domain restraints. The MDFF simulation was conducted with a grid scaling value of 0.5 for 100 ps, followed by 3,000 steps of energy minimization until convergence of the protein RMSD. The MDFF generated model was inspected and manually adjusted in Coot, guided through the use of deep-learning-based amino-acid-wise model quality (DAQ) scoring, and refined in PHENIX.

Data Acquisition
Detector Type	GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)	53.43

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	TFS KRIOS
Minimum Defocus (nm)	1000
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
CTF CORRECTION	CTFFIND
MODEL FITTING	UCSF Chimera
MODEL FITTING	MDFF
INITIAL EULER ASSIGNMENT	cryoSPARC
FINAL EULER ASSIGNMENT	cryoSPARC
RECONSTRUCTION	PHENIX
RECONSTRUCTION	Coot
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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.