Samples at approximately 1 mg/ml were diluted 1/20 immediately prior to application to glow-discharged fenestrated carbon grids. All freezing was done ...
Samples at approximately 1 mg/ml were diluted 1/20 immediately prior to application to glow-discharged fenestrated carbon grids. All freezing was done in cold room. After blotting, samples were plunged into liquid ethane for freezing and stored in liquid nitrogen.
3D Reconstruction
Reconstruction Method
HELICAL
Number of Particles
95
Reported Resolution (Å)
6
Resolution Method
Other Details
Combination of Fourier and real space averaging.
Helical Reconstruction:
A total of 95 repeats from 58 individual tubes were used for
...
Combination of Fourier and real space averaging.
Helical Reconstruction:
A total of 95 repeats from 58 individual tubes were used for
the reconstruction. These tubes fell into 5 helical
symmetries, defined by the Bessel order (n) of the principal
layer lines (1,0) and (0,1). These 5 symmetries were (-23,6),
(-22,6), (-21,6), (-20,6) and (-19,6). For the reference
symmetry (-22,6), the unit cell parameters were:
a= 56.9A,
b=117.1A,
gamma=64.2 deg.
Data within each helical symmetry were averaged in Fourier space
and distortion-correction techniques were applied (Beroukhim and
Unwin, 1997). For each repeat, unit cell parameters were
calculated, and repeats differing by more than 1.5% of the
average value were discarded. The CTF was used to correct
phases and weight amplitudes prior to averaging within each
helical symmetry. Finally, maps were calculated from each of
the averaged datasets. Each of the 2 molecules composing the
unit cell were masked and aligned with the corresponding
molecule from the reference map (-22,6). The maps were
averaged in real-space then back-transformed into Fourier
space. Two-fold symmetry was constrained before calculating
the final map.
Effective resolution of the reconstruction:
The resolution of the final reconstruction was determined to
be 6 A by two methods. First, the dataset was split into two
equal parts and two independant reconstructions were
made. After masking and aligning molecules from these maps,
Fourier shell correlation coefficients and associated phase
residuals were calculated. Secondly, since the crystals had
p2 symmetry, two-fold phase residuals of layer lined datasets
were used to monitor resolution.
Refinement Type
Symmetry Type
HELICAL
Map-Model Fitting and Refinement
Id
1 (1EUL)
Refinement Space
REAL
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
Details
DETAILS--The atomic coordinates of Ca-ATPase (1EUL) were divided into 4 domains
by breaking the peptide at 3 hinge points. Each domain was separately ...
DETAILS--The atomic coordinates of Ca-ATPase (1EUL) were divided into 4 domains
by breaking the peptide at 3 hinge points. Each domain was separately fit into
the electron density map by manual docking using the program O. Besides
matching overall shape, the major criteria involved matching a-helices into
strong columns of density in the map. Whereas cytoplasmic domains were treated
as rigid bodies, elements of the transmembrane domain were bent or displaced to
match strong densities in the cryo-em map. Finally, the loops composing the 3
hinges were rebuilt to reconnect the domains and X-PLOR was used to perform
local energy minimization.
Data Acquisition
Detector Type
KODAK SO-163 FILM
Electron Dose (electrons/Å**2)
10
Imaging Experiment
1
Date of Experiment
2000-01-01
Temperature (Kelvin)
100
Microscope Model
FEI/PHILIPS CM200FEG
Minimum Defocus (nm)
700
Maximum Defocus (nm)
1400
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
2
Imaging Mode
BRIGHT FIELD
Specimen Holder Model
Nominal Magnification
50000
Calibrated Magnification
51300
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
200
Imaging Details
EM Software
Task
Software Package
Version
MODEL FITTING
O
MODEL FITTING
X-PLOR
RECONSTRUCTION
Custom
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
CTF correction of each particle with 4.6% amplitude contrast