6PUZ

Structure of HIV cleaved synaptic complex (CSC) intasome bound with magnesium and INSTI XZ446 (compound 4f)


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3L3U 
experimental modelPDB 1K6Y 
experimental modelPDB 5U1C 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d22.423
f_angle_d0.809
f_chiral_restr0.054
f_bond_d0.007
f_plane_restr0.007
Sample
Assembly of HIV integrase and viral DNA
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentHOMEMADE PLUNGER
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles143698
Reported Resolution (Å)2.8
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC2
Map-Model Fitting and Refinement
Id1 (3L3U, 1K6Y, 5U1C)
Refinement SpaceREAL
Refinement ProtocolFLEXIBLE FIT
Refinement TargetCorrelation coefficient
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)42
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)1500
Maximum Defocus (nm)3000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification37000
Calibrated Magnification63291
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONWarp
IMAGE ACQUISITIONLeginon
CTF CORRECTIONWarp
MODEL FITTINGCoot
MODEL REFINEMENTPHENIX1.16
INITIAL EULER ASSIGNMENTcisTEM1.0
FINAL EULER ASSIGNMENTcisTEM1.0 beta
CLASSIFICATIONcisTEM1.0 beta
RECONSTRUCTIONcisTEM1.0 beta
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION412354