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 7NO2 | pdb_00007no2

Structure of the mature RSV CA lattice: hexamer derived from tubes (C2-symmetric)


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3TIR 
Sample
Rous sarcoma virus - Prague C
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details2.5 seconds blotting time
3D Reconstruction
Reconstruction MethodSUBTOMOGRAM AVERAGING
Number of Particles40962
Reported Resolution (Å)4.3
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC2
Map-Model Fitting and Refinement
Id1 (3TIR)
Refinement SpaceREAL
Refinement ProtocolAB INITIO MODEL
Refinement TargetCorrelation coefficient
Overall B Value
Fitting Procedure
DetailsThree copies of CA monomer were rigid body-fitted into the EM density to accommodate the 3 symmetry independent CA copies. The fit was further refined ...Three copies of CA monomer were rigid body-fitted into the EM density to accommodate the 3 symmetry independent CA copies. The fit was further refined in Coot. The symmetry independent copies were expanded according to the C2 symmetry, and an additional ring of CTDs adjacent to the CA hexamer was added to account for the continuous lattice during the refinement. The model was refined by iterating between automatic real space refinement in Phenix and manual model inspection/editing in Coot.
Data Acquisition
Detector TypeGATAN K2 QUANTUM (4k x 4k)
Electron Dose (electrons/Å**2)3.5
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)1500
Maximum Defocus (nm)4000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification105000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging DetailsAreas of interest for high-resolution data collection were identified in low magnification montages. Prior to tomogram acquisition, gain references were acquired and the filter was fully tuned. Microscope tuning was performed using the FEI AutoCTF software. The ilumination mode used during acquisition was nanoprobe.
EM Software
TaskSoftware PackageVersion
VOLUME SELECTIONMATLABR2018b
VOLUME SELECTIONIMOD4.9
VOLUME SELECTIONDynamo1.1.333
IMAGE ACQUISITIONSerialEM
IMAGE ACQUISITIONDigitalMicrograph
CTF CORRECTIONCTFFIND4.1.10
CTF CORRECTIONIMOD4.9
CTF CORRECTIONNOVACTF
MODEL FITTINGUCSF Chimera1.13.1
MODEL FITTINGCoot0.8.9.1
FINAL EULER ASSIGNMENTDynamo1.1.333
CLASSIFICATIONMATLABR2018b
RECONSTRUCTIONDynamo1.1.333
RECONSTRUCTIONAV3
MODEL REFINEMENTPHENIX1.18
MODEL REFINEMENTCoot0.8.9.1
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTIONCTF-correction was initially performed using ctfphaseflip in IMOD and NovaCTF in the final steps