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)
TypeSourceAccession CodeDetails
experimental modelPDB 3T7A 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP727712% (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 coefficientSolvent content
2.7955.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.567α = 90
b = 110.4β = 90
c = 41.455γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2015-04-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM1.0APS22-BM

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
11.95099.90.11315.766.632965
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.9399.90.6682.426.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT3T7A1.935.5730891201799.760.14480.14130.199Equivalent22.557
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
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.375
r_sphericity_free33.36
r_dihedral_angle_4_deg13.155
r_sphericity_bonded13.065
r_dihedral_angle_3_deg12.461
r_dihedral_angle_1_deg5.264
r_mcangle_it2.514
r_scbond_it2.249
r_rigid_bond_restr2.096
r_mcbond_it1.834
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.375
r_sphericity_free33.36
r_dihedral_angle_4_deg13.155
r_sphericity_bonded13.065
r_dihedral_angle_3_deg12.461
r_dihedral_angle_1_deg5.264
r_mcangle_it2.514
r_scbond_it2.249
r_rigid_bond_restr2.096
r_mcbond_it1.834
r_angle_refined_deg1.327
r_chiral_restr0.107
r_bond_refined_d0.007
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2550
Nucleic Acid Atoms
Solvent Atoms445
Heterogen Atoms112

Software

Software
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing