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Supplementary Information for manuscript # 2003-03-01737
Complete atomic model of the bacterial flagellar filament by electron
cryomicroscopy
Koji Yonekura, Saori Maki-Yonekura & Keiichi Namba
List of files
Name : 2003-03-01737SupFig1.jpg
size : 787 x 621 (142kByte)
type : jpg
Supplementary Figure 1 Stereo view of the middle and upper parts of domain D1 from
inside the filament. The structure of this portion showed little changes from the crystal
structure of F41, and therefore, an appropriate place to check the quality of the density
map. The atomic model of a subunit is superimposed and atoms are coloured coded as:
carbon, yellow; nitrogen, blue; oxygen, red. Prepared with XTALVIEW45 and
RASTER3D46. Contour level of the map is ~ 2.
Name : 2003-03-01737SupFig2.jpg
size : 723 x 1152 (218kByte) type : jpg
Supplementary Figure 2 Stereo diagram of an array of 9 flagellin subunits in the Rtype straight filament. a, Viewed from outside of the filament. b, Viewed from inside
the filament. A flagellin subunit at the centre is coloured red. Prepared with
MOLSCRIPT47 and RASTER3D46.
Name : 2003-03-01737SupFig3ab.jpg
size : 824 x 1111 (283kByte) type : jpg
Name : 2003-03-01737SupFig3cd.jpg
size : 826 x 1128 (268kByte) type : jpg
Supplementary Figure 3 Interactions of flagellin subunits along each direction of the
major helical arrays in the R-type straight filament. a, Along the 11-start; b, along the 5start; c, along the 6-start; d, along the 16-start. Colour scheme of side chains is: positive,
blue; negative, red; polar, black; and hydrophobic, yellow. Each pair of the molecules in
a, b, c and d is shown at the left side in the same subunit array as in Supplementary Fig.
2b. Prepared with MOLSCRIPT47 and RASTER3D46.
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Supplementary Table 1
Data statistics of the flagellar filament
Repeat distance (Å)
1698.8
Basic helix index (n10, l10)
( 11, 4)
(n01, l01)
( -5, 31)
Selection rule
l = 66 n + 361 m
Maximum Bessel order
170
Number of layer-lines
298
Number of averaged images
102
Number of averaged molecules
41,469
Included data in resolution (Å) along the meridian
4.0
along the equator
5.0
3
Resolution (Å)
 ~ 20
20 ~ 15
15 ~ 10
10 ~ 7.0
7.0 ~ 5.0
5.0 ~ 4.0
4.0 ~ 3.0
 ~ 4.0
FOM
Supplementary Table 2 Figure of merit (FOM)# obtained by combination
of the EM phase and the model phase
Sector I*
0.886
0.750
0.677
0.523
0.474
0.429
0.415
0.475
Sector II*
0.908
0.831
0.714
0.552
0.496
0.447
0.432
0.497
Sector III*
0.969
0.666
0.773
0.562
0.500
0.452
0.443
0.506
#
F
N
FOM  
FEM
N
,
(1)
where summation was taken over all N data within a resolution ring, FEM is a structure factor of
the EM data. F is defined as,
F
w PEM ( ) Pcalc( )FEM ( )d

 P
EM
( ) Pcalc( )d
,
(2)
where w is a radial amplitude scaling factor for the EM data against the model data. PEM and
Pcalc represent the phase probability for the EM and model phase, respectively as,
PEM ( ) Pcalc( )  exp[ X 1cos(  EM )] exp[ X 2 cos(  calc)]
,
(3)
where EM and calc refer to the EM and model phase, respectively. By modifying the equation
used in X-ray crystallography44, we define X1 = X2 = X as,
X 
2w  FEM  Fcalc
w  FEM  Fcalc
,
(4)
where Fcalc is a structure factor of the model data.
*Data set in a quadrant was equally divided into three fan-shaped sectors, I, II and III, each
covering an angular range of 30, where sector I is close to the equator, sector II in the middle,
and sector III close to the meridian.