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Crystal structure of Terrestrivirus Inositol pyrophosphatase kinase in complex with ADP and myo-(1OH)IP5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 12% PEG8000, 100mM HEPES pH 7.0, 10mM NaH2PO4, 10% Ethylene Glycol, 5mM ADP and 10mM MgCl2, then soaked in 25% PEG8000, 100mM HEPES pH 7.0, 20% Ethylene Glycol with 5mM myo-(1OH)-IP5, 5mM ADP and 10mM MgCl2
Crystal Properties Matthews coefficient Solvent content 2.8 56.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.841 α = 90 b = 103.835 β = 90 c = 102.719 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 EIGER X 16M 2021-10-14 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) 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 2.6 50 99.4 0.091 0.098 0.036 0.995 8.6 7.1 10770
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 98.8 0.692 0.748 0.273 0.754 6.9
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 FOURIER SYNTHESIS THROUGHOUT 2.6 46.38 9615 525 93.66 0.17761 0.17447 0.2347 0.2063 RANDOM 38.373
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] -0.07 0.02 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.174 r_dihedral_angle_4_deg 24.34 r_dihedral_angle_3_deg 17.522 r_long_range_B_other 7.917 r_long_range_B_refined 7.915 r_dihedral_angle_1_deg 7.652 r_scangle_other 5.903 r_mcangle_other 4.607 r_mcangle_it 4.602 r_scbond_it 3.807
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.174 r_dihedral_angle_4_deg 24.34 r_dihedral_angle_3_deg 17.522 r_long_range_B_other 7.917 r_long_range_B_refined 7.915 r_dihedral_angle_1_deg 7.652 r_scangle_other 5.903 r_mcangle_other 4.607 r_mcangle_it 4.602 r_scbond_it 3.807 r_scbond_other 3.776 r_mcbond_it 2.88 r_mcbond_other 2.845 r_angle_refined_deg 1.616 r_angle_other_deg 1.277 r_chiral_restr 0.079 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 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 1772 Nucleic Acid Atoms Solvent Atoms 58 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling DENZO data reduction PHASER phasing