9QWP | pdb_00009qwp

Structure of the human RalGAP2 complex

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	3.4239
f_angle_d	0.4625
f_chiral_restr	0.0382
f_plane_restr	0.0037
f_bond_d	0.0023

Sample
Homodimer of two RalGAPa2-RalGAPb heterodimers
Sample Components
RalGAP subunit alpha2
RalGAP subunit beta

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

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	420975
Reported Resolution (Å)	3.8
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1
Refinement Space	REAL
Refinement Protocol	AB INITIO MODEL
Refinement Target	cross correlation
Overall B Value	129.72
Fitting Procedure
Details	A model of the RGalpha2/RGbeta complex was calculated using AlphaFold2 running on a local high performance computing cluster (PALMA II), docked into map from 3D reconstruction with ChimeraX and energy optimized with ISOLDE. In an iterative process, the model was optimized using real space refinement in Phenix Refine against the full density map, and manual model building with Coot using the full density map as well as the resampled multi body refinement maps.

Data Acquisition
Detector Type	FEI FALCON IV (4k x 4k)
Electron Dose (electrons/Å**2)	60

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	TFS KRIOS
Minimum Defocus (nm)	500
Maximum Defocus (nm)	4200
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	215000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	crYOLO	1.8.3
IMAGE ACQUISITION	EPU	3.2.0.4776
CTF CORRECTION	RELION	5
MODEL FITTING	UCSF ChimeraX	1.7.dev2023
INITIAL EULER ASSIGNMENT	RELION	5
FINAL EULER ASSIGNMENT	RELION	5
CLASSIFICATION	RELION	5
RECONSTRUCTION	RELION	5
MODEL REFINEMENT	PHENIX	1.21.1_5286
MODEL REFINEMENT	Coot	0.9.8.95
MODEL REFINEMENT	ISOLDE	1.7

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		5519589