3T9E

Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with ADP, 5-(PP)-IP5 (5-IP7) and MgF3 (transition state mimic)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		277	12% (w/v) PEG 3350, 20 mM MgCl2, 0.1 M HEPES, pH 7.0, 1 mM ATP, 2 mM CdCl2, Soaking with 2mM 5-IP7 and 10 mM NaF under pH 5.2 for 2 days , VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.07	α = 90
b = 109.987	β = 90
c = 41.338	γ = 90

Symmetry
Space Group	P 21 21 21

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	MARMOSAIC 225 mm CCD		2011-03-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-BM	1.0	APS	22-BM

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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
1	1.9	50	99.8	0.1	19.6	5.8		32911	-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.93	99.4		0.497	3.2	4.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	FOURIER SYNTHESIS	THROUGHOUT	1.9	37.5	30721	1986	99.3	0.17495	0.17254	0.21263	Equivalent and expanded	18.243

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]
0.27			0.09		-0.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.588
r_dihedral_angle_4_deg	14.469
r_dihedral_angle_3_deg	12.848
r_dihedral_angle_1_deg	5.523
r_scangle_it	2.988
r_scbond_it	1.805
r_angle_refined_deg	1.312
r_mcangle_it	1.271
r_mcbond_it	0.681
r_chiral_restr	0.089

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.588
r_dihedral_angle_4_deg	14.469
r_dihedral_angle_3_deg	12.848
r_dihedral_angle_1_deg	5.523
r_scangle_it	2.988
r_scbond_it	1.805
r_angle_refined_deg	1.312
r_mcangle_it	1.271
r_mcbond_it	0.681
r_chiral_restr	0.089
r_bond_refined_d	0.011
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2604
Nucleic Acid Atoms
Solvent Atoms	494
Heterogen Atoms	76

Software

Software
Software Name	Purpose
HKL-2000	data collection
PHENIX	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	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.