6RNY | pdb_00006rny

PFV intasome - nucleosome strand transfer complex


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3UTB 
experimental modelPDB 3OS0 
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 StatePARTICLE
Vitrification InstrumentLEICA EM CPC
Cryogen NameETHANE
Sample Vitrification Details1 min incubation 3.5s blot
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles177155
Reported Resolution (Å)3.9
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1 (3UTB, 3OS0)
Refinement SpaceREAL
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
DetailsThe initial model was placed in the density using Chimera. Manual building was performed in Coot and final refinement was carried out using phenix.rea ...
Data Acquisition
Detector TypeFEI FALCON II (4k x 4k)
Electron Dose (electrons/Å**2)56
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)1.5
Maximum Defocus (nm)3.5
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification59000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONRELION1.3
IMAGE ACQUISITIONEPU
CTF CORRECTIONCTFFIND1.4
MODEL FITTINGCoot
INITIAL EULER ASSIGNMENTRELION1.3
FINAL EULER ASSIGNMENTRELION1.3
CLASSIFICATIONRELION1.3
RECONSTRUCTIONRELION1.3
MODEL REFINEMENTPHENIX
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION3125