4Q4D | pdb_00004q4d

Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with AMP-PNP and synthetic 3,5-(PP)2-IP4 (3,5-IP8)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3T9F	PDB ENTRY 3T9F

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	277	12% w/v PEG3350, 20 mM magnesium chloride, 0.1 M HEPES, pH 7.0, 1 mM AMP-PNP, 2 mM cadmium chloride, crystals transferred to stabilizing buffer (22% w/v PEG3350, 10 mM magnesium chloride, 0.1 M sodium acetate, pH 5.2) at 277 K overnight (ATP in the crystals was hydrolyzed to ADP) then soaked for three days in stabilizing buffer containing 2 mM 3,5-IP8, VAPOR DIFFUSION, HANGING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.79	α = 90
b = 110.681	β = 90
c = 41.379	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		2014-03-15	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	1.85	50	99.7	0.07	25.7	6.6	35810	35810	-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	1.85	1.88	96.3		0.366	3	4.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	PDB ENTRY 3T9F	1.85	47.01	33431	33431	2197	99.44	0.1819	0.1819	0.17968	0.19	0.21584	0.22	EQUIVALENT AND EXPANDED RANDOM	20.001

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]
0.32			-0.23		-0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.625
r_dihedral_angle_4_deg	17.238
r_dihedral_angle_3_deg	13.08
r_long_range_B_refined	6.686
r_long_range_B_other	6.286
r_dihedral_angle_1_deg	5.531
r_scangle_other	2.445
r_mcangle_it	1.688
r_mcangle_other	1.688
r_angle_refined_deg	1.58
r_scbond_it	1.511
r_scbond_other	1.503
r_mcbond_it	1.003
r_mcbond_other	1.002
r_angle_other_deg	0.75
r_chiral_restr	0.1
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2539
Nucleic Acid Atoms
Solvent Atoms	403
Heterogen Atoms	78

Software

Software
Software Name	Purpose
HKL-2000	data collection
CCP4	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CCP4	phasing