5W2I

Crystal structure of the core catalytic domain of human inositol phosphate multikinase soaked with C4-analogue of PtdIns(4,5)P2 and ADP


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.529835% (w/v) PEG 400, 0.1 M Li2SO4, 100 mM MES Imidanzol buffer , pH 6.0, 50 mM beta-mercaptoethanol at 298K. To obtain complex structures, the apo crystal were further soaked under 35% (w/v) PEG 400, 0.1 M Li2SO4, 100 mM HEPES, pH 7.5 at 298K in the presence of 20 mM C4-analogue of PtdIns(4,5)P2, 10 mM Mg and 5mM ATP for 1 day.
Crystal Properties
Matthews coefficientSolvent content
2.2444.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.09α = 90
b = 78.09β = 90
c = 86.32γ = 90
Symmetry
Space GroupP 42 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300-HS2016-08-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.65099.90.09722.17.736175
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)
11.61.631000.7272.97.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 SYNTHESISTHROUGHOUT1.634.0334007181398.910.171480.169220.21525RANDOM19.146
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]
-0.07-0.070.13
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free34.306
r_dihedral_angle_2_deg31.484
r_sphericity_bonded13.196
r_dihedral_angle_4_deg13.098
r_dihedral_angle_3_deg12.87
r_dihedral_angle_1_deg5.759
r_long_range_B_refined4.861
r_long_range_B_other3.944
r_scangle_other2.126
r_scbond_it1.807
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free34.306
r_dihedral_angle_2_deg31.484
r_sphericity_bonded13.196
r_dihedral_angle_4_deg13.098
r_dihedral_angle_3_deg12.87
r_dihedral_angle_1_deg5.759
r_long_range_B_refined4.861
r_long_range_B_other3.944
r_scangle_other2.126
r_scbond_it1.807
r_scbond_other1.794
r_mcangle_other1.793
r_mcangle_it1.792
r_rigid_bond_restr1.475
r_angle_refined_deg1.393
r_mcbond_it1.259
r_mcbond_other1.256
r_angle_other_deg0.753
r_chiral_restr0.079
r_bond_refined_d0.009
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1943
Nucleic Acid Atoms
Solvent Atoms182
Heterogen Atoms53

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling