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Crystal structure of Zea mays Inositol-tetrakisphosphate Kinase 1 (ITPK1)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 1 M potassium sodium tartrate, 100 mM imidazole, pH 8.0, 200 mM sodium chloride
Crystal Properties Matthews coefficient Solvent content 4.08 69.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.883 α = 90 b = 98.883 β = 90 c = 215.915 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 CCD MARMOSAIC 225 mm CCD 2019-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.0 APS 22-BM
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 2.9 50 98.4 0.068 0.071 0.019 12.7 13 14458
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 2.9 2.95 99.6 0.873 0.907 0.245 0.931 13
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 2.9 49.49 13628 730 98.69 0.1797 0.1771 0.1834 0.2266 0.2272 RANDOM 48.537
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] -0.18 -0.09 -0.18 0.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.034 r_dihedral_angle_3_deg 18.478 r_dihedral_angle_4_deg 14.594 r_dihedral_angle_1_deg 8.569 r_angle_refined_deg 1.794 r_angle_other_deg 1.258 r_chiral_restr 0.082 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.034 r_dihedral_angle_3_deg 18.478 r_dihedral_angle_4_deg 14.594 r_dihedral_angle_1_deg 8.569 r_angle_refined_deg 1.794 r_angle_other_deg 1.258 r_chiral_restr 0.082 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2107 Nucleic Acid Atoms Solvent Atoms 101 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling PDB_EXTRACT data extraction HKL-2000 data collection PHASER phasing