9TIF | pdb_00009tif

Phage 812 baseplate in the pre-contraction state - lower arm


ELECTRON MICROSCOPY
Sample
Staphylococcus phage 812K1/420
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles22031
Reported Resolution (Å)5.6
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement Target
Overall B Value191.1
Fitting Procedure
DetailsFitting of previously refined sub-models (e.g. segment A, segment B, segment C, segment DEF, uRBP1-lRBP2, lRBP1-uRBP2 from the lower arm) in ChimeraX ...Fitting of previously refined sub-models (e.g. segment A, segment B, segment C, segment DEF, uRBP1-lRBP2, lRBP1-uRBP2 from the lower arm) in ChimeraX as rigid bodies, then relaxing the model using ISOLDE before rigid body refinement in Phenix (rigid bodies selected: lid domain of the weld protein, cleaver domains of the hub protein, res. 95-472 of arm scaffold protein and dimers of arm segments A, B and C, dimer of arm segment D, dimer of arm segment E, dimer of arm segment F, trimer of tripod proteins, trimer of RBP1, trimer of RBP2, res. 489-752 of arm scaffold protein).
Data Acquisition
Detector TypeGATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)40.8
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelTFS KRIOS
Minimum Defocus (nm)500
Maximum Defocus (nm)2000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification105000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONTopaz
IMAGE ACQUISITIONSerialEM
CTF CORRECTIONGctf
MODEL FITTINGUCSF ChimeraX1.9
INITIAL EULER ASSIGNMENTRELION5
FINAL EULER ASSIGNMENTRELION5
RECONSTRUCTIONRELION5
MODEL REFINEMENTPHENIX1.21
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING ONLY64874