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Crystal structure of the core catalytic domain of human inositol phosphate multikinase in complex with isorhamnetin
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 isorhamnetin for 3 days.
Crystal Properties Matthews coefficient Solvent content 2.21 44.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.23 α = 90 b = 78.23 β = 90 c = 85.12 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 RAYONIX MX300-HS 2018-04-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.8 50 99.9 0.09 33 15.8 25133 17.74
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.83 99.5 0.989 12.7
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 1.8 40 23722 1275 99.5 0.171 0.168 0.1789 0.224 0.2288 RANDOM 23.87
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] -0.03 -0.03 0.07
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 34.472 r_dihedral_angle_2_deg 33.532 r_sphericity_bonded 19.367 r_dihedral_angle_3_deg 12.131 r_dihedral_angle_4_deg 9.006 r_dihedral_angle_1_deg 5.885 r_long_range_B_refined 4.473 r_long_range_B_other 4.393 r_scangle_other 2.974 r_mcangle_other 2.973
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 34.472 r_dihedral_angle_2_deg 33.532 r_sphericity_bonded 19.367 r_dihedral_angle_3_deg 12.131 r_dihedral_angle_4_deg 9.006 r_dihedral_angle_1_deg 5.885 r_long_range_B_refined 4.473 r_long_range_B_other 4.393 r_scangle_other 2.974 r_mcangle_other 2.973 r_mcangle_it 2.972 r_scbond_other 2.26 r_scbond_it 2.256 r_mcbond_other 2.069 r_mcbond_it 2.067 r_rigid_bond_restr 1.376 r_angle_refined_deg 1.267 r_angle_other_deg 0.864 r_chiral_restr 0.066 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001 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 119 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing