X-RAY DIFFRACTION

Crystallization Details
Method pH Temprature Details
X-RAY DIFFRACTION 7.6 293.15 The enzyme was crystallized at 3.7 mg/ml with a final concentration of 2 mM sodium 2-oxoglutarate, 2 mM ATP and 2 mM MgCl in 25 mM Tris/HCl pH 7.6, 10% v/v glycerol, 150 mM NaCl, 2 mM dithiothreitol. The protein was crystallized fresh without any freezing step, and crystallization was performed through the sitting drop method on a 96-Well MRC 2-Drop Crystallization Plates in polystyrene (SWISSCI, United Kingdom) under anaerobic conditions (N2:H2, gas ratio of 97:3). The crystallization reservoir contained 90 ul of mother liquor (20 % w/v polyethylene glycol 3,350 and 200 mM sodium fluoride). The crystallization drop contained 0.6 ul protein with ligands and 0.6 ul precipitant. Crystals were soaked in the mother liquor supplemented with 20 % v/v glycerol prior to freezing in liquid nitrogen.
Unit Cell:
a: 112.337 Å b: 131.773 Å c: 131.507 Å α: 60.04° β: 87.72° γ: 67.34°
Symmetry:
Space Group: P 1
Crystal Properties:
Matthew's Coefficient: 2.53 Solvent Content: 51.50
Refinement Statistics
Diffraction ID Structure Solution Method Cross Validation Method Resolution Limit (High) Resolution Limit (Low) Number of Reflections (Observed) Number of Reflections (R-free) Percent Reflections (Observed) R-Work R-Free Mean Isotropic
X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.149 42.88 248376 12081 77.0 0.1832 0.2140 38.36
Data Collection
Overall
Resolution Limit (High) Resolution Limit (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
2.148 110.034 92.2 0.110 ? 9.3 3.6 ? 248419 ? ? 35.99
Highest Resolution Shell
# Resolution Limits (Low) Resolution Limits (High) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
1 2.148 2.297 58.8 ? ? 1.3 3.4 ?
Diffraction
Diffraction experiment
Crystal ID Scattering Type Data Collection Temprature Detector Detector Type Details Collection Date Monochromator Protocol
1 100 K ?
Radiation Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X06DA 1.30511 SLS X06DA
Software
Software Name Purpose Version
BUSTER refinement 2.10.4 (21-NOV-2022)
autoPROC data reduction .
STARANISO data scaling .
PHASER phasing .