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Crystal structure of Terrestrivirus inositol pyrophosphate kinase in complex with ADP and 1,4,5-InsP3
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-1,4,5-IP3, 5mM ADP and 10mM MgCl2
Crystal Properties Matthews coefficient Solvent content 2.81 56.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.619 α = 90 b = 100.61 β = 90 c = 105.022 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 2021-12-16 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 2.5 50 99 0.142 0.152 0.054 0.97 8.5 8 12033
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 2.5 2.54 100 0.838 0.894 0.308 0.864 8.3
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 2.5 37.8 11245 606 97.36 0.17593 0.17334 0.177 0.22339 0.2254 RANDOM 36.217
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] 0.02 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.763 r_dihedral_angle_4_deg 23.946 r_dihedral_angle_3_deg 17.274 r_dihedral_angle_1_deg 7.419 r_long_range_B_refined 7.125 r_long_range_B_other 7.124 r_scangle_other 4.179 r_mcangle_it 3.894 r_mcangle_other 3.894 r_scbond_other 2.466
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.763 r_dihedral_angle_4_deg 23.946 r_dihedral_angle_3_deg 17.274 r_dihedral_angle_1_deg 7.419 r_long_range_B_refined 7.125 r_long_range_B_other 7.124 r_scangle_other 4.179 r_mcangle_it 3.894 r_mcangle_other 3.894 r_scbond_other 2.466 r_scbond_it 2.463 r_mcbond_it 2.301 r_mcbond_other 2.259 r_angle_refined_deg 1.442 r_angle_other_deg 1.218 r_chiral_restr 0.106 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 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 1764 Nucleic Acid Atoms Solvent Atoms 117 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling HKL-2000 data reduction PHASER phasing