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Crystal structure of the core catalytic domain of human inositol phosphate multikinase in complex with luteolin
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 2 mM luteolin for 3 days.
Crystal Properties Matthews coefficient Solvent content 2.37 43.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.292 α = 90 b = 78.292 β = 90 c = 85.045 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) Rrim I (All) Rpim I (All) CC (Half) 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 1.75 50 99.9 0.099 0.102 0.025 0.996 30.5 16 27243 16.87
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 1.75 1.78 99.9 0.878 0.909 0.234 0.849 3.12 14.8
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 1.75 36 25710 1377 99.45 0.17671 0.17336 0.1838 0.24099 0.2477 RANDOM 27.036
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] 0.35 0.35 -0.7
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 36.101 r_dihedral_angle_2_deg 35.172 r_sphericity_bonded 27.943 r_dihedral_angle_4_deg 13.335 r_dihedral_angle_3_deg 12.972 r_dihedral_angle_1_deg 6.649 r_long_range_B_refined 5.154 r_long_range_B_other 5.062 r_mcangle_other 3.78 r_mcangle_it 3.779
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 36.101 r_dihedral_angle_2_deg 35.172 r_sphericity_bonded 27.943 r_dihedral_angle_4_deg 13.335 r_dihedral_angle_3_deg 12.972 r_dihedral_angle_1_deg 6.649 r_long_range_B_refined 5.154 r_long_range_B_other 5.062 r_mcangle_other 3.78 r_mcangle_it 3.779 r_scangle_other 3.622 r_scbond_it 2.77 r_scbond_other 2.769 r_mcbond_other 2.699 r_mcbond_it 2.696 r_angle_refined_deg 1.294 r_rigid_bond_restr 1.232 r_angle_other_deg 0.9 r_chiral_restr 0.074 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 21
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling