<supp> Supplementary Information

Table Data statistics

crystal / native / Se-Met
peak / edge / remote

Crystallographic data

Beam Line / PF BL18B / PF BL18B
Space group / P6322 / R32
Wavelength (Å) / 1.0000 / 0.9795 / 0.9797 / 0.9803
Resolution (Å) / 1.70(1.79-1.70) / 2.30(2.42-2.30) / 2.30(2.42-2.30) / 2.30(2.42-2.30)
Number of Reflections
Observed / 266,163(17,767) / 128,483(113,22) / 141,293(20,517) / 141,050(20,583)
Unique / 41,139(3,901) / 12,358(1,690) / 12,509(1,805) / 12,487(1,803)
Completeness (%) / 91.3(61.0) / 99.1(94.5) / 100.0(100.0) / 100.0(100.0)
Averaged redundancy / 6.5(4.5) / 10.4(6.7) / 11.3(11.4) / 11.3(11.4)
Averaged I/(I) / 6.5(2.5) / 8.2(4.6) / 7.7(3.7) / 7.8(3.6)
aRmerge / 0.08(0.31) / 0.08(0.19) / 0.09(0.22) / 0.087(0.23)
bRlambda / - / 0.028 / 0.031 / -

Phasing

cPhasing power
Iso / - / 0.544 / 0.776 / -
Ano / - / 3.782 / 3.098 / 1.203
dRcullis_iso / - / 0.71 / 0.61 / -
eOverall figure of merit / - / 0.568

Refinement

Resolution (Å) / 20-1.70 / - / - / -
Total number of
non-hydrogen atoms
Protein / 2271
Others / 273
Solvent / 266
fR-factor / 0.1811
gRfree-Factor / 0.2040
bonds (Å) / 0.008
bond-angle (˚) / 1.417
Averaged B-factor (Å2) / 18.58
hRamachandran analysis (%)
Most favored / 90.2
Additionally allowed / 9.4
generously allowed / 0.4

Values in the parentheses are for the highest resolution shell.

aRmeas=h [m/(m-1)]1/2j|<Ih-Ih,j|/hj Ih,j, where <Ih is the mean intensities of symmetry-equivalent reflections and m is redundancy.

bRlambda=||Fj|-|Fo||/|F0|, where Fjis the structure factor of the data collected at j, and F0 is the structure factor collected at 0.9803Å

cPhasing power = | FH(calc)| / phase-integrated lack of closure.

dRCullis = phase-integrated lack of closure / | FPH – FP | .

eFigure of merit after the initial phasing using the program SHARP

fR-factor = |Fobs –Fcalc| / Fobs, where Fobs and Fcalc are observed and calculated structure factor amplitudes.

gRfree-factor was calculated as for R-factor, using a random 10 % subset from all reflections.

hRamachandran plot was calculated by PROCHECK.

Structure determination and refinement

All of crystals that were used to collect diffraction data were flash-frozen after being soaked into a cryoprotectant consisting of 15% (v/v) glycerol and mother liquor. For phasing calculation, 2.3Å resolution multiwavelength anomalous diffraction (MAD) data were collected at peak (0.9795 Å), edge (0.9797 Å) of selenium K-edge and remote (0.9803 Å) wavelengths. Out of 11 selenium atom sites, 4 sites were initially located using the program SOLVE. After the initial experimental phases with 4 selenium atom sites were calculated, 7 additional sites were found by the difference Fourier method using SHARP. A model including 299 out of 339 residues was built manually using the program O from a density map which was re-phased with all 11 selenium atom sites and modified with solvent flattening by program SHARP/SOLOMON at 2.3Å resolution. After several rounds of molecular dynamic refinement by the program CNS using MAD data, with manual fitting using the program O, the model was transferred to the native crystal by molecular replacement using the program AMoRe. The molecular dynamic refinement performed using the program CNS with calculating the Rfree factor from the 10% test datasetrandomly selected in order to monitor refinement. The topology and parameter files of the pyruvate and magnesium moieties were obtained from the HIC-up site. This model was checked using the program PROCHECK. Of 299 resides in the model, 90.1 % are in the most favored regions, 9.4 % are in additional allowedregions (with1 residue are in generously allowed regions) in the Ramachandran plot. The one N-terminal and 40 C-terminal residues are not able to be modeled because of their flexibility.