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Crystal structure of Terrestrivirus Inositol pyrophosphatase kinase in complex with ADP and scyllo-L-(1,2,3,4)-IP4
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 L-scyllo- (1,2,3,4)IP4, 5mM ADP and 10mM MgCl2
Crystal Properties Matthews coefficient Solvent content 2.85 56.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.671 α = 90 b = 103.415 β = 90 c = 103.674 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 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 1.95 50 99.3 0.062 0.065 0.019 0.995 12.5 11.1 25569
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 1.95 1.98 99.5 0.747 0.785 0.237 0.881 10.8
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 1.95 48.52 24214 1290 99.14 0.16573 0.16409 0.19619 0.2185 RANDOM 22.73
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] -0.04 0.03 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.596 r_dihedral_angle_4_deg 30.011 r_dihedral_angle_3_deg 15.318 r_long_range_B_refined 7.733 r_long_range_B_other 7.697 r_dihedral_angle_1_deg 6.979 r_scangle_other 5.946 r_scbond_it 3.963 r_scbond_other 3.833 r_mcangle_it 3.595
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.596 r_dihedral_angle_4_deg 30.011 r_dihedral_angle_3_deg 15.318 r_long_range_B_refined 7.733 r_long_range_B_other 7.697 r_dihedral_angle_1_deg 6.979 r_scangle_other 5.946 r_scbond_it 3.963 r_scbond_other 3.833 r_mcangle_it 3.595 r_mcangle_other 3.594 r_mcbond_it 2.451 r_mcbond_other 2.435 r_angle_refined_deg 1.873 r_angle_other_deg 1.499 r_chiral_restr 0.103 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 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 222 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling DENZO data reduction PHASER phasing