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Crystal structure of the core catalytic domain of human inositol phosphate multikinase soaked with C4-analogue of PtdIns(4,5)P2 and ADP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 298 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 structures, the apo crystal were further soaked under 35% (w/v) PEG 400, 0.1 M Li2SO4, 100 mM HEPES, pH 7.5 at 298K in the presence of 20 mM C4-analogue of PtdIns(4,5)P2, 10 mM Mg and 5mM ATP for 1 day.
Crystal Properties Matthews coefficient Solvent content 2.24 44.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.09 α = 90 b = 78.09 β = 90 c = 86.32 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 2016-08-05 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 1.6 50 99.9 0.097 22.1 7.7 36175
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 100 0.727 2.9 7.3
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 1.6 34.03 34007 1813 98.91 0.17148 0.16922 0.1964 0.21525 0.2331 RANDOM 19.146
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] -0.07 -0.07 0.13
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 34.306 r_dihedral_angle_2_deg 31.484 r_sphericity_bonded 13.196 r_dihedral_angle_4_deg 13.098 r_dihedral_angle_3_deg 12.87 r_dihedral_angle_1_deg 5.759 r_long_range_B_refined 4.861 r_long_range_B_other 3.944 r_scangle_other 2.126 r_scbond_it 1.807
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 34.306 r_dihedral_angle_2_deg 31.484 r_sphericity_bonded 13.196 r_dihedral_angle_4_deg 13.098 r_dihedral_angle_3_deg 12.87 r_dihedral_angle_1_deg 5.759 r_long_range_B_refined 4.861 r_long_range_B_other 3.944 r_scangle_other 2.126 r_scbond_it 1.807 r_scbond_other 1.794 r_mcangle_other 1.793 r_mcangle_it 1.792 r_rigid_bond_restr 1.475 r_angle_refined_deg 1.393 r_mcbond_it 1.259 r_mcbond_other 1.256 r_angle_other_deg 0.753 r_chiral_restr 0.079 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.001 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 1943 Nucleic Acid Atoms Solvent Atoms 182 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling