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Crystal structure of Zea mays Inositol-tetrakisphosphate Kinase 1 mutant (ZmITPK1-H192A)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 12% PEG3350, 100mM HEPES 7.0, 200mM CaAc2 and 10% Glycerol
Crystal Properties Matthews coefficient Solvent content 3.77 67.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.161 α = 90 b = 98.161 β = 90 c = 202.43 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 2020-12-12 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 2.85 50 98.6 0.085 0.089 0.025 12 12.9 14039
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 2.85 2.9 98.8 0.816 0.848 0.228 0.915 13.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.85 47.74 13136 700 97.51 0.2269 0.2244 0.271 0.2784 RANDOM 53.865
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] -0.03 -0.01 -0.03 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.848 r_dihedral_angle_3_deg 19.972 r_dihedral_angle_4_deg 13.339 r_dihedral_angle_1_deg 9.199 r_angle_refined_deg 1.897 r_angle_other_deg 1.266 r_chiral_restr 0.085 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.848 r_dihedral_angle_3_deg 19.972 r_dihedral_angle_4_deg 13.339 r_dihedral_angle_1_deg 9.199 r_angle_refined_deg 1.897 r_angle_other_deg 1.266 r_chiral_restr 0.085 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2069 Nucleic Acid Atoms Solvent Atoms 16 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling PDB_EXTRACT data extraction xia2 data reduction PHASER phasing