7SJ4 | pdb_00007sj4

Human Trio residues 1284-1959 in complex with Rac1

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2NZ8

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	9.563
f_angle_d	0.414
f_chiral_restr	0.041
f_plane_restr	0.003
f_bond_d	0.002

Sample
Human Trio residues 1284-1959 in complex with Rac1

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	Blot force 10

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	922202
Reported Resolution (Å)	2.86
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (2NZ8, 2NZ8)
Refinement Space	REAL
Refinement Protocol	RIGID BODY FIT
Refinement Target	correlation coefficient
Overall B Value
Fitting Procedure
Details	The initial model was generated from the pdb structure (2NZ8) using the SWISS-MODEL server and rigid-body fitted using Chimera. Several runs of structure refinement were done using the coot and phenix real-space refinement.

Data Acquisition
Detector Type	GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)	55

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	1000
Maximum Defocus (nm)	3000
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	3.3.1
IMAGE ACQUISITION	Leginon
CTF CORRECTION	cryoSPARC	3.3.1
MODEL FITTING	UCSF Chimera	1.15
MODEL FITTING	Coot	9.6
MODEL REFINEMENT	Coot	9.6
MODEL REFINEMENT	PHENIX	1.20-4459
INITIAL EULER ASSIGNMENT	cryoSPARC	3.3.1
FINAL EULER ASSIGNMENT	cryoSPARC	3.3.1
CLASSIFICATION	cryoSPARC	3.3.1
RECONSTRUCTION	cryoSPARC	3.3.1

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