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Crystal structure of the core catalytic domain of human inositol phosphate multikinase in complex with quercetin
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 quercetin for 3 days.
Crystal Properties Matthews coefficient Solvent content 2.18 43.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.956 α = 90 b = 77.956 β = 90 c = 84.468 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 1.85 50 99.9 0.096 0.099 0.025 0.998 30.7 16.2 22745 17.57
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 1.88 100 0.827 0.853 0.207 0.888 3.77 16.6
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 5W2G 1.85 40 21533 1161 99.61 0.17668 0.17366 0.23445 0.2289 RANDOM 24.991
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] -0.26 -0.26 0.52
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 41.322 r_dihedral_angle_2_deg 33.231 r_sphericity_bonded 20.023 r_dihedral_angle_3_deg 12.703 r_dihedral_angle_4_deg 9.515 r_dihedral_angle_1_deg 6.03 r_long_range_B_refined 4.44 r_long_range_B_other 4.335 r_scangle_other 2.991 r_mcangle_other 2.944
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 41.322 r_dihedral_angle_2_deg 33.231 r_sphericity_bonded 20.023 r_dihedral_angle_3_deg 12.703 r_dihedral_angle_4_deg 9.515 r_dihedral_angle_1_deg 6.03 r_long_range_B_refined 4.44 r_long_range_B_other 4.335 r_scangle_other 2.991 r_mcangle_other 2.944 r_mcangle_it 2.943 r_scbond_it 2.272 r_scbond_other 2.271 r_mcbond_it 2.086 r_mcbond_other 2.082 r_angle_refined_deg 1.29 r_rigid_bond_restr 1.076 r_angle_other_deg 0.896 r_chiral_restr 0.07 r_bond_refined_d 0.008 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 122 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling