Table 1.
A. Data collection | |||
Data set | Binary complex | Ternary complex | Se-Met (peak) |
X-ray source | PF NW12A | PLS BL-4A | PLS BL-4A |
Wavelength (Å) | 1.00000 | 1.23990 | 0.97954 |
Space group | P321 | P321 | P321 |
a, b, c (Å) | 136.3, 136.3, 79.92 | 136.3, 136.3, 79.83 | 136.3, 136.3, 83.28 |
α, β, γ (°) | 90, 90, 120 | 90, 90, 120 | 90, 90, 120 |
Resolution range (Å) | 50–2.50 (2.59–2.50)a | 50–1.77 (1.80–1.77)a | 50–2.73 (2.80–2.73)a |
Total/unique reflections | 489 231/29 916 | 1 660 636/82 927 | 731 176/23 991 |
Completeness (%) | 100.0 (100.0)a | 99.8 (96.5)a | 100.0 (100.0)a |
I/σI | 39.5 (8.5)a | 80.7 (8.3)a | 45.5 (7.7)a |
Rmerge b (%) | 12.5 (41.7)a | 6.1 (41.9)a | 16.5 (65.5)a |
B. Phasing | |||
Figure of merit for 20.0–3.10 Å range (before/after density modification) | 0.30/0.72 | ||
C. Model refinement | |||
Resolution range (Å) | 20.0–2.50 | 20.0–1.77 | 20.0–2.73 |
Rwork/Rfree c (%) | 18.1/23.1 | 18.0/20.5 | 19.0/24.7 |
Number of atoms/average B-factor (Å2) | |||
Protein nonhydrogen atoms | 4556/27.7 | 4563/22.5 | 4603/36.7 |
Water oxygen atoms | 324/28.0 | 791/37.1 | 199/36.8 |
Ligand nonhydrogen atoms | |||
Fe(III) ion | 1/43.4 | 1/17.5 | 1/45.8 |
2-Oxoglutarate | 10/21.8 | ||
Sulfate | 20/51.5 | 20/46.4 | |
Glycerol | 6/58.8 | 6/44.0 | |
R.M.S. deviations from ideal geometry | |||
Bond lengths (Å)/angles (°) | 0.008/1.21 | 0.007/1.07 | 0.010/1.25 |
Ramachandran plot | |||
Most favorable (%) | 89.5 | 90.3 | 89.3 |
Allowed (%) | 9.9 | 9.7 | 10.5 |
Generously allowed (%) | 0.6 | 0.0 | 0.2 |
Disallowed (%) | 0.0 | 0.0 | 0.0 |
aValues in parentheses refer to the highest resolution shell.
bRmerge = ∑h∑i | I(h)i – <I(h)> | /∑h∑i I(h)i, where I(h) is the intensity of reflection h, ∑h is the sum over all reflections, and ∑i is the sum over i measurements of reflection h.
cRwork = ∑ | |Fobs| – |Fcalc| | /∑ |Fobs|, where Rfree is calculated for a randomly chosen 5% of reflections, which were not used for structure refinement and Rwork is calculated for the remaining reflections.