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Crystal structure of the core catalytic domain of human inositol phosphate multikinase in complex with compound 2
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 10 mM compound 2 for 3 days
Crystal Properties Matthews coefficient Solvent content 2.16 43.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.219 α = 90 b = 78.219 β = 90 c = 84.324 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 2022-03-21 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 99.7 0.067 0.069 0.018 0.996 42.5 15.2 26853
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 0.669 0.693 0.178 0.939 4.96 14.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 1.75 39.14 25389 1367 99.41 0.19152 0.18883 0.24219 0.2415 RANDOM 34.331
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] 1.69 1.69 -3.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.366 r_long_range_B_refined 9.426 r_long_range_B_other 8.885 r_rigid_bond_restr 8.414 r_dihedral_angle_1_deg 6.304 r_dihedral_angle_2_deg 6.21 r_mcangle_it 4.819 r_mcangle_other 4.817 r_scangle_other 4.569 r_mcbond_it 3.445
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.366 r_long_range_B_refined 9.426 r_long_range_B_other 8.885 r_rigid_bond_restr 8.414 r_dihedral_angle_1_deg 6.304 r_dihedral_angle_2_deg 6.21 r_mcangle_it 4.819 r_mcangle_other 4.817 r_scangle_other 4.569 r_mcbond_it 3.445 r_mcbond_other 3.445 r_scbond_it 3.351 r_scbond_other 3.35 r_angle_refined_deg 0.924 r_angle_other_deg 0.428 r_chiral_restr 0.048 r_bond_refined_d 0.005 r_bond_other_d 0.004 r_gen_planes_refined 0.004 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 179 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling