Skip to main content

 3J83 | pdb_00003j83

Heptameric EspB Rosetta model guided by EM density


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4WJ1 
Sample
Mycobacterial protein
Specimen Preparation
Sample Aggregation StatePARTICLE
Staining TypeNEGATIVE
Staining Materialuranyl formate
Staining Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles1455
Reported Resolution (Å)30
Resolution MethodFSC 0.5 CUT-OFF
Other DetailsInitial reconstructions were determined from a side-view 2D average based on observed 7-fold symmetry of the top view using a rotational extrusion met ...Initial reconstructions were determined from a side-view 2D average based on observed 7-fold symmetry of the top view using a rotational extrusion method. The initial model was then refined in 6 iterations with EMAN2 using untilted particles. (Single particle--Applied symmetry: C7)
Refinement Type
Symmetry TypePOINT
Point SymmetryC7
Map-Model Fitting and Refinement
Id1 (4WJ1)
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement TargetRMSD / Rosetta score
Overall B Value
Fitting Procedure
DetailsREFINEMENT PROTOCOL--rigid body DETAILS--Homology model generated from PDB coordinates and used for symmetric docking in Rosetta.
Data Acquisition
Detector TypeFEI EAGLE (4k x 4k)
Electron Dose (electrons/Å**2)25
Imaging Experiment1
Date of Experiment2013-08-28
Temperature (Kelvin)298
Microscope ModelFEI TECNAI SPIRIT
Minimum Defocus (nm)800
Maximum Defocus (nm)1200
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging ModeBRIGHT FIELD
Specimen Holder ModelSIDE ENTRY, EUCENTRIC
Nominal Magnification49000
Calibrated Magnification65900
SourceLAB6
Acceleration Voltage (kV)120
Imaging DetailsLow dose
EM Software
TaskSoftware PackageVersion
MODEL FITTINGRosetta
RECONSTRUCTIONEMAN2
RECONSTRUCTIONSPIDER