Experiment: 9B62

Human RANBP2/RAN(GTP)/RANGAP1-SUMO1/UBC9/CRM1/RAN(GTP) - composite map and model

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3UIN
experimental model	PDB	3GJX
experimental model	PDB	4L6E
experimental model	PDB	1K5D

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	10.589
f_angle_d	0.436
f_chiral_restr	0.037
f_bond_d	0.003
f_plane_restr	0.003

Sample
Human RANBP2/RAN(GTP)/RANGAP1-SUMO1/UBC9/CRM1/RAN(GTP) complex

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	30 s wait time, blot for 2.5 s before plunging

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	534708
Reported Resolution (Å)	2.9
Resolution Method	OTHER
Other Details	Composite map - estimated best average resolution of FR maps 2.9 Related particles and maps used to generate the composite listed in Related Entries
Refinement Type
Symmetry Type	POINT

Map-Model Fitting and Refinement
Id	1 (3uin, 3gjx, 4l6e, 1k5d)
Refinement Space	REAL
Refinement Protocol	OTHER
Refinement Target
Overall B Value
Fitting Procedure
Details	Atomic model was manually fit and refined using composite map, and manually inspected using Coot

Data Acquisition
Detector Type	GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)	85.2

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
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	RELION
IMAGE ACQUISITION	SerialEM
CTF CORRECTION	Gctf
MODEL REFINEMENT	PHENIX	1.19.2_4158:

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		895509	This is a composite map so numbers of particles per map component differs - after selection of particles containing Crm1 there were 704835 unique particles - after selection of particles containing Crm1-Ran(GTP) there were 534708 unique particles