4V5X | pdb_00004v5x

The cryo-EM structure of a 3D DNA-origami object

ELECTRON MICROSCOPY

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Sample
POINTER-SHAPED 3D DNA- ORIGAMI OBJECT

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

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	28502
Reported Resolution (Å)	11.5
Resolution Method	FSC 0.143 CUT-OFF
Other Details	TWO MODELS WERE REFINED INDEPENDENTLY TO PREVENT OVERFITTING THROUGH GOLD-STANDARD FOURIER-SHELL CORRELATIONS. THERE IS A MISSING COVALENT BOND BETWEEN THE LAST BASE OF THIS PDB FILE AND THE FIRST ONE IN PDB ENTRY 2YMG. IN ADDITION THERE IS A COVALENT BOND BETWEEN THE FIRST BASE IN THIS FILE AND THE LAST IN 2YMG GIVING A CIRCULAR MOLECULE. IN TOTAL THERE ARE FIVE PDB FILES. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2210.(DEPOSITION ID: 11146).
Refinement Type	HALF-MAPS REFINED INDEPENDENTLY
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1
Refinement Space	RECIPROCAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details	METHOD--MOLECULAR DYNAMICS FLEXIBLE FITTING REFINEMENT PROTOCOL--THEORETICAL

Data Acquisition
Detector Type	FEI FALCON I (4k x 4k)
Electron Dose (electrons/Å**2)	10

Imaging Experiment	1
Date of Experiment	2012-04-01
Temperature (Kelvin)	80
Microscope Model	FEI POLARA 300
Minimum Defocus (nm)	890
Maximum Defocus (nm)	4460
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification	31000
Calibrated Magnification	39436
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
CTF CORRECTION	CTFFIND	3
RECONSTRUCTION	RELION

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
	WIENER FILTER (RELION)