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Crystal structure of the core catalytic domain of human inositol phosphate multikinase in complex with myricetin
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 myricetin for 3 days.
Crystal Properties Matthews coefficient Solvent content 2.17 43.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.717 α = 90 b = 77.717 β = 90 c = 84.465 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 1.9 50 99.6 0.123 0.13 0.04 0.977 16.9 9.7 20939 16.83
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 1.9 1.93 100 0.728 0.768 0.241 0.88 4 9.6
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 1.9 50 19777 1068 99.32 0.17689 0.17337 0.1822 0.24428 0.2509 RANDOM 24.725
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] -0.24 -0.24 0.47
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 43.736 r_dihedral_angle_2_deg 36.511 r_sphericity_bonded 22.157 r_dihedral_angle_4_deg 13.652 r_dihedral_angle_3_deg 12.921 r_dihedral_angle_1_deg 6.457 r_long_range_B_refined 4.953 r_long_range_B_other 4.789 r_mcangle_it 3.29 r_mcangle_other 3.289
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 43.736 r_dihedral_angle_2_deg 36.511 r_sphericity_bonded 22.157 r_dihedral_angle_4_deg 13.652 r_dihedral_angle_3_deg 12.921 r_dihedral_angle_1_deg 6.457 r_long_range_B_refined 4.953 r_long_range_B_other 4.789 r_mcangle_it 3.29 r_mcangle_other 3.289 r_scangle_other 3.114 r_scbond_it 2.394 r_scbond_other 2.393 r_mcbond_it 2.371 r_mcbond_other 2.37 r_rigid_bond_restr 1.487 r_angle_refined_deg 1.31 r_angle_other_deg 0.907 r_chiral_restr 0.071 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 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 1935 Nucleic Acid Atoms Solvent Atoms 177 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling