9QCV | pdb_00009qcv

Cryo-EM structure of CAK-CDK2-cyclin A2 bound to AMP-PNP

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8P6Y
experimental model	PDB	1OKV

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	8.862
f_angle_d	0.548
f_chiral_restr	0.041
f_plane_restr	0.004
f_bond_d	0.003

Sample
CAK-CDK2-cyclin A2 complex
Sample Components
CDK-activating kinase (CAK)
CDK2-cyclin A2

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	282506
Reported Resolution (Å)	2.5
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT

Map-Model Fitting and Refinement
Id	1 (8P6Y, 1OKV)
Refinement Space	REAL
Refinement Protocol	RIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)	50

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	TFS KRIOS
Minimum Defocus (nm)	400
Maximum Defocus (nm)	2200
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	130000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cryoSPARC
IMAGE ACQUISITION	EPU
CTF CORRECTION	cryoSPARC
CTF CORRECTION	RELION	4.0
MODEL FITTING	UCSF ChimeraX
INITIAL EULER ASSIGNMENT	RELION	4.0
FINAL EULER ASSIGNMENT	RELION	4.0
CLASSIFICATION	RELION	4.0
RECONSTRUCTION	RELION	4.0
MODEL REFINEMENT	PHENIX	1.21-5207

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