Structure of beta-galactosidase at 3.2-A resolution obtained by cryo-electron microscopy
ELECTRON MICROSCOPY
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 ...
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 mode ...
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.