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Human inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic domain in complex with beta-D-glucopyranosyl 1,3,4-trisphosphate/AMP-PNP/Mg
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1W2C Chain A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 0.81 M sodium citrate, 0.1M Tris pH 8.5 and 0.1 M NaCl.
Protein:precipitant ratio 1:1.
Protein concentration: 18 mg/ml.
Protein buffer: 20 mM Tris pH 7.5, 50 mM ammonium sulfate and 2 mM DTT.
Soaking 2h with 1.5 M lithium sulfate, 0.1 M Tris pH 8.5, 5 mM ligand, 3 mM AMP-PNP and 3 mM MgCl2.
Crystal Properties Matthews coefficient Solvent content 2.71 54.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.815 α = 90 b = 97.587 β = 90 c = 191.929 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M KB mirrors, rectangular beam shape 2021-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979264 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 48.84 96.8 0.04 0.994 12 10.5 56714 29.545
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.89 74.3 0.263 0.779 2.2 7.2
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 48.84 53680 2986 96.63 0.19735 0.19563 0.2031 0.22779 0.2331 RANDOM 42.004
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] 0.82 0.61 -1.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.943 r_dihedral_angle_4_deg 16.653 r_dihedral_angle_3_deg 16.578 r_long_range_B_refined 7.243 r_long_range_B_other 7.179 r_dihedral_angle_1_deg 6.343 r_scangle_other 4.73 r_mcangle_other 3.872 r_mcangle_it 3.87 r_scbond_it 2.932
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.943 r_dihedral_angle_4_deg 16.653 r_dihedral_angle_3_deg 16.578 r_long_range_B_refined 7.243 r_long_range_B_other 7.179 r_dihedral_angle_1_deg 6.343 r_scangle_other 4.73 r_mcangle_other 3.872 r_mcangle_it 3.87 r_scbond_it 2.932 r_scbond_other 2.89 r_mcbond_it 2.506 r_mcbond_other 2.499 r_angle_refined_deg 1.356 r_angle_other_deg 1.256 r_chiral_restr 0.064 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4355 Nucleic Acid Atoms Solvent Atoms 364 Heterogen Atoms 140
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling REFMAC phasing Coot model building PDB_EXTRACT data extraction