4Q4C

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3T9FPDB ENTRY 3T9F

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP727712% w/v PEG3350, 20 mM magnesium chloride, 0.1 M HEPES, pH 7.0, 1 mM ATP, 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 1,5-IP8, VAPOR DIFFUSION, HANGING DROP
Crystal Properties
Matthews coefficientSolvent content
2.7254.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.519α = 90
b = 110.224β = 90
c = 41.381γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2014-03-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.0APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.95099.20.06922.24.93319133191-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.9395.90.34633.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 3T9F1.946.983081730817200998.950.163460.163460.161610.19211EQUIVALENT AND EXPANDED20.49
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]
0.280.05-0.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.352
r_dihedral_angle_4_deg12.578
r_dihedral_angle_3_deg12.24
r_long_range_B_refined6.48
r_long_range_B_other6.081
r_dihedral_angle_1_deg5.704
r_scangle_other2.196
r_mcangle_it1.623
r_mcangle_other1.622
r_angle_refined_deg1.566
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.352
r_dihedral_angle_4_deg12.578
r_dihedral_angle_3_deg12.24
r_long_range_B_refined6.48
r_long_range_B_other6.081
r_dihedral_angle_1_deg5.704
r_scangle_other2.196
r_mcangle_it1.623
r_mcangle_other1.622
r_angle_refined_deg1.566
r_scbond_other1.438
r_scbond_it1.437
r_mcbond_it0.962
r_mcbond_other0.959
r_angle_other_deg0.735
r_chiral_restr0.093
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms2604
Nucleic Acid Atoms
Solvent Atoms454
Heterogen Atoms76

Software

Software
Software NamePurpose
HKL-2000data collection
CCP4model building
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing