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Crystal structure of Zea mays Inositol-tetrakisphosphate Kinase 1 mutant (ZmITPK1-H192A) in complex with InsP6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 12% PEG3350, 100 mM HEPES, 7.0, 200 mM calcium chloride, 10% glycerol
Crystal Properties Matthews coefficient Solvent content 4.09 69.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.07 α = 90 b = 99.07 β = 90 c = 215.444 γ = 120
Symmetry Space Group P 61 2 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 PIXEL DECTRIS EIGER X 16M 2020-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.6 50 99.7 0.066 0.07 0.023 15.5 9.9 20094
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 2.6 2.64 99.8 0.849 0.891 0.269 0.881 10.6
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 SAD THROUGHOUT 2.6 42.11 18995 996 99.3 0.2047 0.2021 0.2103 0.2517 0.2544 RANDOM 43.691
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] -0.24 -0.12 -0.24 0.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.214 r_dihedral_angle_3_deg 18.77 r_dihedral_angle_4_deg 15.643 r_dihedral_angle_1_deg 8.956 r_angle_refined_deg 1.928 r_angle_other_deg 1.278 r_chiral_restr 0.103 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.214 r_dihedral_angle_3_deg 18.77 r_dihedral_angle_4_deg 15.643 r_dihedral_angle_1_deg 8.956 r_angle_refined_deg 1.928 r_angle_other_deg 1.278 r_chiral_restr 0.103 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2184 Nucleic Acid Atoms Solvent Atoms 95 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling PDB_EXTRACT data extraction HKL-2000 data collection PHASER phasing