6RNY

PFV intasome - nucleosome strand transfer complex

ELECTRON MICROSCOPY

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Sample
Nucleosome core particle bound by PFV intasome post in the post catalytic state
Sample Components
Nucleosome
Integrase
Human DNA
DNA

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	LEICA EM CPC
Cryogen Name	ETHANE
Sample Vitrification Details	1 min incubation 3.5s blot

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	177155
Reported Resolution (Å)	3.9
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (3UTB, 3OS0)
Refinement Space	REAL
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
Details	The initial model was placed in the density using Chimera. Manual building was performed in Coot and final refinement was carried out using phenix.real_space_refine and namdinator. Additional restraints describing protein secondary structure, DNA base pairing and stacking were used in Phenix.

Data Acquisition
Detector Type	FEI FALCON II (4k x 4k)
Electron Dose (electrons/Å**2)	56

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	1.5
Maximum Defocus (nm)	3.5
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	59000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	RELION	1.3
IMAGE ACQUISITION	EPU
CTF CORRECTION	CTFFIND	1.4
MODEL FITTING	Coot
INITIAL EULER ASSIGNMENT	RELION	1.3
FINAL EULER ASSIGNMENT	RELION	1.3
CLASSIFICATION	RELION	1.3
RECONSTRUCTION	RELION	1.3
MODEL REFINEMENT	PHENIX

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		3125