TABLE 4.
Results of fitting the structural components of DAF into the cryoEM difference density map
| Modela | Sumfb | Clash (%)c | −Den (%)d | Orientation (o)e
|
Center (Å)f
|
Sumf as a function of SCR
|
|||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| thet1 | thet2 | thet3 | centx | centy | centz | SCR1 | SCR2 | SCR3 | SCR4 | ||||
| 10JVa | 19.0 | 0.0 | 18.5 | 227.8 | 29.8 | 135.2 | 38.2 | 6.6 | 151.1 | 11.9 | 19.6 | 17.8 | 26.2 |
| 10JVb | 20.3 | 0.0 | 16.6 | 216.0 | 43.8 | 139.8 | 38.6 | 6.9 | 151.4 | 14.1 | 20.0 | 20.6 | 26.2 |
| 10JWa | 21.3 | 0.0 | 15.8 | 241.5 | 22.5 | 121.5 | 39.8 | 8.3 | 151.8 | 13.3 | 23.4 | 21.7 | 26.2 |
| 10JWb | 20.8 | 0.0 | 16.1 | 225.0 | 32.0 | 135.0 | 39.3 | 7.4 | 150.9 | 11.9 | 24.2 | 18.7 | 27.4 |
| 10JYa | 20.8 | 0.0 | 17.1 | 225.0 | 13.5 | 135.0 | 40.1 | 8.5 | 150.8 | 11.3 | 24.5 | 18.3 | 27.8 |
| 10JYb | 14.6 | 8.1 | 10.8 | 139.2 | 16.5 | 210.0 | 37.1 | 16.0 | 131.5 | 21.7 | 17.3 | 10.2 | 9.0 |
| 10JYc | 20.4 | 1.3 | 8.6 | 223.5 | 11.5 | 135.0 | 41.0 | 9.2 | 150.9 | 12.2 | 20.4 | 20.0 | 28.8 |
| 10JYd | 18.5 | 0.0 | 9.0 | 240.0 | 347.8 | 120.0 | 43.3 | 9.6 | 150.3 | 11.1 | 19.7 | 13.0 | 29.1 |
| XR23 | 30.6 | 0.0 | 10.4 | 244.8 | 79.8 | 132.2 | 40.0 | 17.5 | 150.5 | 0.0 | 31.0 | 30.1 | 0.0 |
| NMR23 | 30.0 | 0.0 | 2.3 | 241.5 | 15.0 | 120.0 | 36.2 | 13.8 | 149.2 | 0.0 | 26.0 | 33.2 | 0.0 |
| SCR1 | 23.7 | 0.0 | 1.9 | 345.0 | 3.0 | 15.0 | 76.4 | 37.8 | 148.8 | 23.7 | 0.0 | 0.0 | 0.0 |
| SCR4 | 31.7 | 0.0 | 2.4 | 235.5 | 0.5 | 120.0 | 6.4 | −31.6 | 156.6 | 0.0 | 0.0 | 0.0 | 31.8 |
Lukacik et al. (25) provide eight different X-ray crystallography structures of DAF from three different crystal forms: two structures of 10JC, designated a and b; two structures from 10JW, designated a and b; and four structures from 10JY, designated a, b, c, and d. XR corresponds to the X-ray crystallographic coordinates for SCR2 and -3 from 10JVa. NMR23 is the first of 42 conformers submitted by Uhrinova et al. (60).
Sumf is defined as the average value of density for all nonhydrogen atomic positions normalized by setting the highest density in the map to 100.
Clash represents the percentage of atoms in the model that have steric clashes with symmetry-related subunits.
−Den provides the percentage of atoms that are positioned in negative density.
Orientation Eulerian angles that rotate the standard orientation of the model into the cryoEM density are given in degrees as described by Rossmann (40).
x, y, and z are the three translational positions of the mass center for the fitted model.