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Crystal structure of the core catalytic domain of human inositol phosphate multikinase in complex with compound 4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5W2I
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 compound 4 for 3 days
Crystal Properties Matthews coefficient Solvent content 2.18 43.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.94 α = 90 b = 77.94 β = 90 c = 85.565 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 2022-09-22 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 1.85 50 99.1 0.114 0.119 0.031 0.997 20.39 11.4 23240
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 1.85 1.88 98.6 0.771 0.819 0.268 0.779 2.21 8.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.85 46.38 21483 1162 97.88 0.17576 0.17294 0.1815 0.22942 0.2411 RANDOM 23.625
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] 1.49 1.49 -2.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.818 r_dihedral_angle_1_deg 6.366 r_long_range_B_refined 3.935 r_long_range_B_other 3.7 r_dihedral_angle_2_deg 3.501 r_rigid_bond_restr 3.096 r_mcangle_it 2.348 r_mcangle_other 2.347 r_scangle_other 2.31 r_scbond_it 1.752
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.818 r_dihedral_angle_1_deg 6.366 r_long_range_B_refined 3.935 r_long_range_B_other 3.7 r_dihedral_angle_2_deg 3.501 r_rigid_bond_restr 3.096 r_mcangle_it 2.348 r_mcangle_other 2.347 r_scangle_other 2.31 r_scbond_it 1.752 r_scbond_other 1.751 r_mcbond_it 1.646 r_mcbond_other 1.645 r_angle_refined_deg 0.923 r_angle_other_deg 0.31 r_chiral_restr 0.042 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1939 Nucleic Acid Atoms Solvent Atoms 157 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling