Find PDB structures and Computed Structure Models (CSM) by combining queries from tools in this suite: Attribute Search, Sequence Similarity, Sequence Motif, 3D Similarity, and 3D Motif with 'AND' logic.
Venezuelan Equine Encephalitis Virus TC83 strain E1 protein
Venezuelan Equine Encephalitis Virus TC83 strain E2 protein
Venezuelan Equine Encephalitis Virus TC83 strain capsid protein
Specimen Preparation
Sample Aggregation State
PARTICLE
Vitrification Instrument
FEI VITROBOT MARK I
Cryogen Name
ETHANE
Sample Vitrification Details
vitrification carried out in Chiu lab, Houston, TX
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
37000
Reported Resolution (Å)
4.8
Resolution Method
FSC 0.5 CUT-OFF
Other Details
After each iteration, the non-icosahedral parts (which included the lipids and the RNA) in the reconstruction were removed by a soft-edged mask derive ...
After each iteration, the non-icosahedral parts (which included the lipids and the RNA) in the reconstruction were removed by a soft-edged mask derived from an icosahedrally organized, protein-only map that was low-pass filtered to 30 Angstroms. This map then served as the reference model for the next iteration.
Refinement Type
Symmetry Type
POINT
Point Symmetry
I
Map-Model Fitting and Refinement
Id
1 (3N40)
2 (3N40)
3 (1EP5)
Refinement Space
REAL
Refinement Protocol
FLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details
METHOD--all-atom refinement REFINEMENT PROTOCOL--all-atom refinement against
cryo-EM density DETAILS--ROSETTA was used to refine the full-length E1 a ...
METHOD--all-atom refinement REFINEMENT PROTOCOL--all-atom refinement against
cryo-EM density DETAILS--ROSETTA was used to refine the full-length E1 and E2
and all of the structured part of CP. ROSETTA uses the cryo-EM density as a
restraint, along with energy minimization, to eliminate steric clashes and
assure proper molecular geometry.
Data Acquisition
Detector Type
GATAN ULTRASCAN 4000 (4k x 4k)
Electron Dose (electrons/Å**2)
18
Imaging Experiment
1
Date of Experiment
2008-04-09
Temperature (Kelvin)
96
Microscope Model
JEOL 3200FSC
Minimum Defocus (nm)
400
Maximum Defocus (nm)
2500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
4.3
Imaging Mode
BRIGHT FIELD
Specimen Holder Model
JEOL 3200FSC CRYOHOLDER
Nominal Magnification
100000
Calibrated Magnification
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
300
Imaging Details
omega energy filter
EM Software
Task
Software Package
Version
MODEL FITTING
Rosetta
RECONSTRUCTION
EMAN
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
CTF parameters were determined from particles within each CCD image