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Crystal structure of the core catalytic domain of human inositol phosphate multikinase in complex with an inhibitor UNC7467
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 5 mM compound for 3 days
Crystal Properties Matthews coefficient Solvent content 2.17 43.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.224 α = 90 b = 78.224 β = 90 c = 84.815 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 2020-07-17 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 1.7 50 99.6 0.053 49.913 12.6 29472
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.73 0.839 0.86
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 1.7 37.309 29242 1571 98.897 0.208 0.2054 0.2194 0.2485 0.2607 25.734
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] 1.067 1.067 -2.135
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 18.215 r_lrange_other 16.633 r_dihedral_angle_6_deg 14.716 r_dihedral_angle_3_deg 13.535 r_dihedral_angle_2_deg 11.17 r_scangle_it 8.671 r_scangle_other 8.668 r_mcangle_it 8.314 r_mcangle_other 8.314 r_dihedral_angle_1_deg 6.447
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 18.215 r_lrange_other 16.633 r_dihedral_angle_6_deg 14.716 r_dihedral_angle_3_deg 13.535 r_dihedral_angle_2_deg 11.17 r_scangle_it 8.671 r_scangle_other 8.668 r_mcangle_it 8.314 r_mcangle_other 8.314 r_dihedral_angle_1_deg 6.447 r_rigid_bond_restr 5.947 r_scbond_it 5.751 r_scbond_other 5.751 r_mcbond_it 5.276 r_mcbond_other 5.261 r_angle_refined_deg 1.787 r_angle_other_deg 0.606 r_nbd_refined 0.231 r_nbd_other 0.23 r_xyhbond_nbd_refined 0.224 r_symmetry_nbd_other 0.194 r_nbtor_refined 0.193 r_symmetry_xyhbond_nbd_refined 0.173 r_symmetry_nbd_refined 0.158 r_chiral_restr 0.085 r_symmetry_nbtor_other 0.079 r_symmetry_xyhbond_nbd_other 0.041 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1918 Nucleic Acid Atoms Solvent Atoms 125 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling