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Crystal structure of the core catalytic domain of human inositol phosphate multikinase in complex with diosmetin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5W2G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 35% (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 coefficient Solvent content 2.36 43.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.971 α = 90 b = 77.971 β = 90 c = 85.362 γ = 90
Symmetry Space Group P 42 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 225 mm CCD 2017-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1 APS 22-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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2 50 99.5 0.09 0.096 0.032 22.3 7.8 18315 22.79
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) Redundancy Number Unique Reflections (All) 1 2 2.03 100 0.896 0.955 0.317 0.786 2.8 8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 5w2g 2 38 17172 947 98.62 0.17644 0.17314 0.1828 0.23949 0.2511 RANDOM 30.474
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] 0.31 0.31 -0.63
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 46.746 r_dihedral_angle_2_deg 34.649 r_sphericity_bonded 27.046 r_dihedral_angle_4_deg 16.013 r_dihedral_angle_3_deg 13.7 r_dihedral_angle_1_deg 5.469 r_long_range_B_refined 4.5 r_long_range_B_other 4.241 r_mcangle_other 2.752 r_mcangle_it 2.749
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 46.746 r_dihedral_angle_2_deg 34.649 r_sphericity_bonded 27.046 r_dihedral_angle_4_deg 16.013 r_dihedral_angle_3_deg 13.7 r_dihedral_angle_1_deg 5.469 r_long_range_B_refined 4.5 r_long_range_B_other 4.241 r_mcangle_other 2.752 r_mcangle_it 2.749 r_scangle_other 2.541 r_scbond_it 1.942 r_scbond_other 1.941 r_mcbond_other 1.851 r_mcbond_it 1.848 r_angle_refined_deg 1.208 r_angle_other_deg 0.879 r_rigid_bond_restr 0.694 r_chiral_restr 0.065 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 1941 Nucleic Acid Atoms Solvent Atoms 134 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling