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PDB Id
Uniprot Id
Source Organism
Host Organism
Protein Name
Method
Summary
Structure Feature
Experiment
Ligands & Environment
9QWP
pdb_00009qwp
10.2210/pdb9qwp/pdb
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FASTA
PDB
MMCIF
Binary MMCIF
XML
Structure Factors
Full Validation Report
Validation File (XML)
Validation File (CIF)
FASTA Zipped(.gz)
PDB Zipped(.gz)
MMCIF Zipped(.gz)
Binary MMCIF Zipped(.gz)
Structure Factors Zipped(.gz)
Validation File Zipped (.xml.gz)
Validation File Zipped (.cif.gz)
ELECTRON MICROSCOPY
Sample
Homodimer of two RalGAPa2-RalGAPb heterodimers
Specimen Preperation
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
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
Date of Experiment
?
Temprature (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
?
Imaging Experiment
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
?
