3J7H

Structure of beta-galactosidase at 3.2-A resolution obtained by cryo-electron microscopy

ELECTRON MICROSCOPY

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Sample
Escherichia coli beta-galactosidase

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	LEICA EM GP
Cryogen Name	ETHANE
Sample Vitrification Details	Blot for 2 seconds before plunging into liquid ethane (LEICA EM GP).

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	11726
Reported Resolution (Å)	3.2
Resolution Method	FSC 0.143 CUT-OFF
Other Details	Reconstruction details: 24,750 particles were picked automatically from the best 509 micrographs by detecting the local maxima of correlation of each image with a Gaussian disk of 100 Angstrom in radius and extracted using a binning factor of 2 and a box size of 384x384 pixels. Particles were then subjected to reference-free 2D classification in EMAN2. 160 classes out of a total of 250 were used for de novo initial model determination using e2initialmodel.py and imposing D2 symmetry. A subset of 23,452 particles (corresponding to the 160 classes used for the initial model building) was then used for 3D refinement using a gold-standard approach. Two stacks of 11,726 particles each were independently subjected to eight rounds of iterative refinement in FREALIGN using a high-resolution frequency limit of 8 Angstrom and using the best 50% of particles from each stack according to phase residual values (equivalent to 5,863 particles) to calculate the reconstructions at each iteration. At this point particles were re-extracted from the original unbinned micrographs using a box size of 768x768 pixels and further refined in FREALIGN starting from the most recent set of alignments obtained with the binned data. The final map was obtained by averaging the two half-reconstructions in real space and corrected by a B-factor of -85 Angstrom^2 for the purpose of visualization.
Refinement Type	HALF-MAPS REFINED INDEPENDENTLY
Symmetry Type	POINT
Point Symmetry	D2

Map-Model Fitting and Refinement
Id	1
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details	METHOD--Local refinement, Flexible fitting DETAILS--Initial local fitting was done using Chimera and then COOT was used for flexible fitting and model building.

Data Acquisition
Detector Type	GATAN K2 (4k x 4k)
Electron Dose (electrons/Å**2)	45

Imaging Experiment	1
Date of Experiment	2013-10-31
Temperature (Kelvin)	79.7
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	1000
Maximum Defocus (nm)	2500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.7
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification	105000
Calibrated Magnification	105000
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details	Parallel beam illumination

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

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
	Individual frames of each movie were aligned by cross-correlation using the cumulative average of previously aligned frames as a reference to align the remaining frames. Parameters of the contrast transfer function for each micrograph were estimated from power spectra obtained using periodogram averaging with tiles of size 512x512 pixels extracted from all frames of each movie. These power spectra were then radially averaged and used to estimate the defocus for each image using frequencies in the 15.0-3.0 Angstrom range. CTF correction was done for each particle as implemented in FREALIGN's reconstruction protocol.