8QJE

Neck of phage 812 virion (C12)


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d4.833
f_angle_d0.573
f_chiral_restr0.043
f_bond_d0.004
f_plane_restr0.004
Sample
Staphylococcus phage 812
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE-PROPANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles16293
Reported Resolution (Å)4.16
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC12
Map-Model Fitting and Refinement
Id1
Refinement SpaceREAL
Refinement ProtocolAB INITIO MODEL
Refinement Targetcross-correlation coefficient
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeFEI FALCON II (4k x 4k)
Electron Dose (electrons/Å**2)49
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)1200
Maximum Defocus (nm)2400
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification75000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONEMAN2
IMAGE ACQUISITIONEPU
CTF CORRECTIONGctf1.0.6
MODEL FITTINGCoot0.9
MODEL REFINEMENTPHENIX1.19
MODEL REFINEMENTISOLDE1.4
INITIAL EULER ASSIGNMENTRELION3.1
FINAL EULER ASSIGNMENTRELION3.1
CLASSIFICATIONRELION3.1
RECONSTRUCTIONRELION3.1
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION23947Manual particle selection