5BYA

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

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3T7A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	277	12% (w/v) PEG 3350, 20 mM MgCl2, 0.1 M HEPES, pH 7.0, 1 mM ATP and 2 mM CdCl2. The crystals were transferred to a stabilizing buffer containing 22% (w/v) PEG 3350, 10 mM MgCl2, 0.1 M sodium acetate, pH 5.2 at 4 oC overnight, while ATP in the crystals was hydrolyzed to ADP. The crystals were soaked under the above stabilizing buffer for three days with 2 mM analog.

Crystal Properties
Matthews coefficient	Solvent content
2.79	55.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.567	α = 90
b = 110.4	β = 90
c = 41.455	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		2015-04-10	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	99.9	0.113	15.76	6.6		32965

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	1.9	1.93	99.9		0.668	2.42	6.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	3T7A	1.9	35.57	30891	2017	99.76	0.1448	0.1413	0.199	Equivalent	22.557

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]
0.6			-0.3		-0.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.375
r_sphericity_free	33.36
r_dihedral_angle_4_deg	13.155
r_sphericity_bonded	13.065
r_dihedral_angle_3_deg	12.461
r_dihedral_angle_1_deg	5.264
r_mcangle_it	2.514
r_scbond_it	2.249
r_rigid_bond_restr	2.096
r_mcbond_it	1.834

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.375
r_sphericity_free	33.36
r_dihedral_angle_4_deg	13.155
r_sphericity_bonded	13.065
r_dihedral_angle_3_deg	12.461
r_dihedral_angle_1_deg	5.264
r_mcangle_it	2.514
r_scbond_it	2.249
r_rigid_bond_restr	2.096
r_mcbond_it	1.834
r_angle_refined_deg	1.327
r_chiral_restr	0.107
r_bond_refined_d	0.007
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2550
Nucleic Acid Atoms
Solvent Atoms	445
Heterogen Atoms	112

Software

Software
Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	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.