3T9F

Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with ADP and 1,5-(PP)2-IP4 (1,5-IP8)

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 5-IP7 under pH 5.2 for 2 days , VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.036	α = 90
b = 110.009	β = 90
c = 41.484	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 300 mm CCD		2011-02-09	M	SINGLE WAVELENGTH

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

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	2	50	92.4	0.126	17.7	4.4		26099	-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	2	2.03	92.4		33.7	4	2.8

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	2	38.82	24344	1606	91.53	0.17556	0.17301	0.21409	Equivalent and expanded	17.699

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]
0.44			0.11		-0.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.3
r_dihedral_angle_4_deg	15.688
r_dihedral_angle_3_deg	13.587
r_dihedral_angle_1_deg	5.571
r_scangle_it	3.331
r_scbond_it	2.036
r_angle_refined_deg	1.39
r_mcangle_it	1.33
r_mcbond_it	0.7
r_chiral_restr	0.091

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.3
r_dihedral_angle_4_deg	15.688
r_dihedral_angle_3_deg	13.587
r_dihedral_angle_1_deg	5.571
r_scangle_it	3.331
r_scbond_it	2.036
r_angle_refined_deg	1.39
r_mcangle_it	1.33
r_mcbond_it	0.7
r_chiral_restr	0.091
r_bond_refined_d	0.011
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2547
Nucleic Acid Atoms
Solvent Atoms	400
Heterogen Atoms	77

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 R01GM133198.