ELECTRON MICROSCOPY Experimental Data



EM Sample
Sample Concentration (mg/ml) 0.05
Sample pH 7.4
Sample Vitrification Details 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.
Sample Aggregation State FILAMENT
Name of Sample Ca2+-ATPase tubular crystals
Sample Details Crystals formed in presence of decavanadate and thapsigargin
EM Data Acquisition
Date of Experiment 2000-01-01
Num of Micrographs-Images Used 58
Temperature (Kelvin) 100.0
Microscope Model FEI/Philips CM200FEG/T
Detector Type KODAK SO163 FILM
Minimum Defocus (nm) 700.0
Maximum Defocus (nm) 1400.0
Minimum Tilt Angle (degrees) 0.0
Maximum Tilt Angle (degrees) 0.0
Nominal CS 2.0
Imaging Mode BRIGHT FIELD
Electron Dose (electrons nm**-2) 1000.0
Illumination Mode FLOOD BEAM
Nominal Magnification 50000
Calibrated Magnification 51300
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 200
Imaging Details --
3D Reconstruction
Software Package(s)
Reconstruction Method helical reconstruction
EM Image Reconstruction Statistics
Number of Particles 95
Actual Pixel Size 2.53
Effective Resolution 6.0
CTF Correction Method CTF correction of each particle with 4.6% amplitude contrast
EM Reconstruction Magnification Callibration light harvesting complex crystals
Other Details 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.
EM Map-Model Fitting and Refinement
Refinement Space Refinement Protocol Refinement Target Overall B Value Fitting Procedure Fitting Software
REAL -- -- -- -- O