1KJU

Ca2+-ATPase in the E2 State

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1EUL

Sample
Ca2+-ATPase tubular crystals

Specimen Preparation
Sample Aggregation State	HELICAL ARRAY
Vitrification Instrument
Cryogen Name
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.

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 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 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