5DGH

Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with AMP-PNP and 5-(PCP)-IP5


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 AMP-PNP 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. The crystals were soaked under the above stabilizing buffer for three days with 2 mM compound.
Crystal Properties
Matthews coefficientSolvent content
2.6653.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.9α = 90
b = 110.34β = 90
c = 41.253γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2015-06-12MSINGLE 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
12.15096.80.08316.54.823365
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)
12.12.3587.20.3822.53

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 SYNTHESISTHROUGHOUT3T7A2.129.0421891142996.650.189450.186710.2314Equivalent and expanded24.654
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]
0.31-0.01-0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.917
r_dihedral_angle_3_deg14.047
r_dihedral_angle_4_deg11.566
r_long_range_B_refined6.328
r_dihedral_angle_1_deg5.761
r_mcangle_it2.791
r_scbond_it1.751
r_mcbond_it1.59
r_angle_refined_deg1.45
r_chiral_restr0.098
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.917
r_dihedral_angle_3_deg14.047
r_dihedral_angle_4_deg11.566
r_long_range_B_refined6.328
r_dihedral_angle_1_deg5.761
r_mcangle_it2.791
r_scbond_it1.751
r_mcbond_it1.59
r_angle_refined_deg1.45
r_chiral_restr0.098
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2539
Nucleic Acid Atoms
Solvent Atoms266
Heterogen Atoms108

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data scaling