5INJ

Crystal Structure of Prenyltransferase PriB Ternary Complex with L-Tryptophan and Dimethylallyl thiolodiphosphate (DMSPP)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5293.15PriB was crystallized by sitting drop vapor diffusion method by 1:1 v/v mixing of 10 mg/mL PriB solution in the presence of 1 mM L-Tryptophan with reservoir solution containing 0.1 M Tris pH 8.5, 20% w/v PEG 3350, 0.1 M MgCl2. The mixed drops of 0.4-1 uL were equilibrated over a reservoir solution of 50 uL and incubated at 20oC in the dark. The ternary complex was obtained by 1:1.5 v/v soaking a solution of substrate mimic 25 mM Dimethylallyl S-thiolodiphosphate (DMSAPP), 0.05 M Tris pH 8.5, 10% w/v PEG 3350, 0.05 M MgCl2 into PriB crystals. The iodine derivative was prepared by 1:3 v/v soaking a solution of 0.5 M sodium iodide, 0.05 M Tris pH 8.5, 10% w/v PEG 3350, 0.05 M MgCl2 into PriB crystals
Crystal Properties
Matthews coefficientSolvent content
2.0239.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 105.396α = 90
b = 83.422β = 106.74
c = 41.618γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HE2015-08-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.97931APS31-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rrim I (All)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.18628.8296.20.0750.0750.0986.63.565094
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.41.4887.20.6561.22.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADFREE R-VALUE1.428.8161.3465074200096.10.1630.1620.197Random Selection23.3976
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2681
Nucleic Acid Atoms
Solvent Atoms532
Heterogen Atoms70

Software

Software
Software NamePurpose
SCALAdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
AutoSolphasing