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Crystal Structure of Human Inositol 1,3,4-Trisphosphate 5/6-Kinase (ITPK1) in Complex with ADP and Mn2+
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 277 0.1M NA CITRATE PH 5.6, 0.2M K/NA TARTRATE, 2M (NH4)2SO4 , VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.46 49.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.704 α = 90 b = 94.315 β = 90 c = 130.242 γ = 90
Symmetry Space Group P 21 21 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 CCD ADSC QUANTUM 4 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 1.0 ALS 5.0.3
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 1.8 50 94.4 0.063 26.2 4.4 68169
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 MOLECULAR REPLACEMENT THROUGHOUT 1.8 50 64701 3416 94.38 0.18333 0.18097 0.1797 0.22926 0.2281 RANDOM 24.31
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] 1.31 -0.48 -0.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.014 r_dihedral_angle_4_deg 19.624 r_dihedral_angle_3_deg 15.668 r_dihedral_angle_1_deg 6.928 r_scangle_it 6.022 r_scbond_it 4.247 r_mcangle_it 4.131 r_mcbond_it 2.927 r_angle_refined_deg 1.67 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.014 r_dihedral_angle_4_deg 19.624 r_dihedral_angle_3_deg 15.668 r_dihedral_angle_1_deg 6.928 r_scangle_it 6.022 r_scbond_it 4.247 r_mcangle_it 4.131 r_mcbond_it 2.927 r_angle_refined_deg 1.67 r_nbtor_refined 0.313 r_nbd_refined 0.216 r_symmetry_vdw_refined 0.203 r_symmetry_hbond_refined 0.175 r_xyhbond_nbd_refined 0.148 r_chiral_restr 0.123 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5366 Nucleic Acid Atoms Solvent Atoms 527 Heterogen Atoms 118
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction