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Crystal structure of Terrestrivirus Inositol pyrophosphatase kinase in complex with ADP and scyllo-IP6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 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 scyllo-IP6, 5mM ADP and 10mM MgCl2
Crystal Properties Matthews coefficient Solvent content 2.78 55.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.214 α = 90 b = 103.123 β = 90 c = 103.846 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 2021-11-02 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 2.45 50 99.5 0.083 0.088 0.029 0.992 9.9 9.1 12643
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 2.45 2.49 98.7 0.718 0.762 0.247 0.872 8.4
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 2.46 37.42 11078 603 91.85 0.18275 0.18022 0.1913 0.2282 0.2331 RANDOM 37.019
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] -0.06 -0.03 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.622 r_dihedral_angle_4_deg 25.92 r_dihedral_angle_3_deg 17.582 r_long_range_B_refined 10.182 r_long_range_B_other 9.92 r_dihedral_angle_1_deg 8.047 r_scangle_other 6.978 r_mcangle_other 5.312 r_mcangle_it 5.311 r_scbond_it 4.652
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.622 r_dihedral_angle_4_deg 25.92 r_dihedral_angle_3_deg 17.582 r_long_range_B_refined 10.182 r_long_range_B_other 9.92 r_dihedral_angle_1_deg 8.047 r_scangle_other 6.978 r_mcangle_other 5.312 r_mcangle_it 5.311 r_scbond_it 4.652 r_scbond_other 4.48 r_mcbond_it 3.432 r_mcbond_other 3.406 r_angle_refined_deg 1.841 r_angle_other_deg 1.334 r_chiral_restr 0.113 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 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 1766 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms 69
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling DENZO data reduction PHASER phasing