4CCT | pdb_00004cct

Dengue 1 cryo-EM reconstruction

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1TG8

Sample
MATURE DENGUE VIRUS 1

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	LIQUID ETHANE

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	6412
Reported Resolution (Å)	4.5
Resolution Method
Other Details	FTER MODELING THE STRUCTURES WERE REGULARIZED USING MOLECULAR DYNAMICS WITH FLEXIBLE MOLECULAR DYNAMICS WITH FLEXIBLE FITTING PROTOCOL. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2142.(DEPOSITION ID: 10897).
Refinement Type
Symmetry Type	POINT
Point Symmetry	I

Map-Model Fitting and Refinement
Id	1 (1TG8)
Refinement Space	REAL
Refinement Protocol	OTHER
Refinement Target
Overall B Value
Fitting Procedure
Details	METHOD--LOCAL CORRELATION REFINEMENT PROTOCOL--X-RAY

Data Acquisition
Detector Type	GATAN ULTRASCAN 4000 (4k x 4k)
Electron Dose (electrons/Å**2)	18

Imaging Experiment	1
Date of Experiment	2011-12-16
Temperature (Kelvin)	100
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	989
Maximum Defocus (nm)	3441
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.7
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification	75000
Calibrated Magnification	75000
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
MODEL FITTING	UCSF Chimera
RECONSTRUCTION	EMAN	1
RECONSTRUCTION	EMAN	2

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
	WIENER FILTER WEIGHTING EACH PARTICLE DURING 3D RECONSTRUCTION