9B3I | pdb_00009b3i

Cryo-EM structure of yeast (Nap1)2-H2A-H2B-Kap114-RanGTP

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8F1E
experimental model	PDB	9B3F

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	8.358
f_angle_d	0.754
f_chiral_restr	0.048
f_plane_restr	0.007
f_bond_d	0.006

Sample
Complex of Kap114 bound to Ran GTPase Gsp1, H2A-H2B and Nap1

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	133516
Reported Resolution (Å)	2.88
Resolution Method	FSC 0.143 CUT-OFF
Other Details	Composite map was generated by first applying vop multiply to the particle subtraction mask and the consensus volume (covering Kap114 and RanGTP), then composited with locally refined region for the Nap1 and Histone region by vop maximum in Chimera X.
Refinement Type
Symmetry Type	POINT

Map-Model Fitting and Refinement
Id	1 (8F1E, 9B3F)
Refinement Space
Refinement Protocol	OTHER
Refinement Target
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	FEI FALCON IV (4k x 4k)
Electron Dose (electrons/Å**2)	50

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	900
Maximum Defocus (nm)	2200
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification	165000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cryoSPARC
IMAGE ACQUISITION	SerialEM
CTF CORRECTION	cryoSPARC
MODEL FITTING	UCSF ChimeraX
MODEL FITTING	Coot
INITIAL EULER ASSIGNMENT	cryoSPARC
FINAL EULER ASSIGNMENT	cryoSPARC
CLASSIFICATION	cryoSPARC
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	PHENIX	1.19.1_4122:

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		1381753	Blob picker then followed by Topaz picking.