7U06 | pdb_00007u06

Structure of the yeast TRAPPII-Rab11/Ypt32 complex in the closed/open state (composite structure)

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3CUE
experimental model	PDB	3RWO
experimental model	PDB	3PR6

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	5.9699
f_angle_d	0.8173
f_chiral_restr	0.0474
f_plane_restr	0.0056
f_bond_d	0.0046

Sample
TRAPPII complex bound to Rab11/Ypt32

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	The sample was incubated on the grid for 10 seconds followed by blotting for 5 seconds before plunging in liquid ethane.

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	149906
Reported Resolution (Å)	4.2
Resolution Method	FSC 0.143 CUT-OFF
Other Details	The composite map was generated by combining the consensus dimer map (EMD-26233) with focused refinement maps deposited in the entries EMD-26234, EMD-26235, EMD-26236, EMD-26237, EMD-26238, EMD-26239, EMD-26240, EMD-26241, EMD-26242, EMD-26243, EMD-26244, EMD-26245, EMD-26246, EMD-26247, EMD-26248, EMD-26249, EMD-26250, EMD-26251, EMD-26252 and EMD-26253 using Combine Focused Maps in Phenix.
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (3CUE, 3RWO, 3PR6)
Refinement Space	REAL
Refinement Protocol	OTHER
Refinement Target
Overall B Value
Fitting Procedure
Details	Model was rebuilt in coot and refined using phenix.real_space_refine.

Data Acquisition
Detector Type	GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)	53

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TALOS ARCTICA
Minimum Defocus (nm)	800
Maximum Defocus (nm)	2500
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	63000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	200
Imaging Details

EM Software
Task	Software Package	Version
IMAGE ACQUISITION	EPU
CTF CORRECTION	cryoSPARC	3.2.0
CTF CORRECTION	RELION	3.1
MODEL FITTING	Coot
MODEL REFINEMENT	PHENIX
INITIAL EULER ASSIGNMENT	cryoSPARC	3.2.0
FINAL EULER ASSIGNMENT	RELION	3.1
RECONSTRUCTION	PHENIX

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		979187