5INJ

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

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293.15	PriB 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 coefficient	Solvent content
2.02	39.06

Crystal Data

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

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	RAYONIX MX225HE		2015-08-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.97931	APS	31-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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.186	28.82	96.2	0.075	0.075	0.098	6.6	3.5		65094

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.4	1.48	87.2		0.656	1.2	2.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	FREE R-VALUE	1.4	28.816	1.34	65074	2000	96.1	0.163	0.162	0.197	Random Selection	23.3976

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 Atoms	Number
Protein Atoms	2681
Nucleic Acid Atoms
Solvent Atoms	532
Heterogen Atoms	70

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
AutoSol	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.