6M8D

Crystal structure of the core catalytic domain of human inositol phosphate multikinase in complex with diosmetin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5W2G 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP629835% (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 structure, the apo crystal was further soaked under 35% (w/v) PEG 400, 0.1 M Li2SO4, 100 mM HEPES, pH 7.5 at 298K in the presence of 10 mM diosmetin for 3 days.
Crystal Properties
Matthews coefficientSolvent content
2.3643.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.971α = 90
b = 77.971β = 90
c = 85.362γ = 90
Symmetry
Space GroupP 42 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2017-10-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM1APS22-BM

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
125099.50.090.0960.03222.37.81831522.79
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.031000.8960.9550.3170.7862.88

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 SYNTHESISTHROUGHOUT5w2g2381717294798.620.176440.173140.23949RANDOM30.474
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]
0.310.31-0.63
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free46.746
r_dihedral_angle_2_deg34.649
r_sphericity_bonded27.046
r_dihedral_angle_4_deg16.013
r_dihedral_angle_3_deg13.7
r_dihedral_angle_1_deg5.469
r_long_range_B_refined4.5
r_long_range_B_other4.241
r_mcangle_other2.752
r_mcangle_it2.749
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free46.746
r_dihedral_angle_2_deg34.649
r_sphericity_bonded27.046
r_dihedral_angle_4_deg16.013
r_dihedral_angle_3_deg13.7
r_dihedral_angle_1_deg5.469
r_long_range_B_refined4.5
r_long_range_B_other4.241
r_mcangle_other2.752
r_mcangle_it2.749
r_scangle_other2.541
r_scbond_it1.942
r_scbond_other1.941
r_mcbond_other1.851
r_mcbond_it1.848
r_angle_refined_deg1.208
r_angle_other_deg0.879
r_rigid_bond_restr0.694
r_chiral_restr0.065
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.002
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 Atoms1941
Nucleic Acid Atoms
Solvent Atoms134
Heterogen Atoms22

Software

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