☰ Navigation Tabs
Crystal structure of Terrestrivirus Inositol pyrophosphatase kinase in complex with ADP and scyllo-IP5
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-IP5, 5mM ADP and 10mM MgCl2
Crystal Properties Matthews coefficient Solvent content 2.82 56.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.562 α = 90 b = 103.358 β = 90 c = 104.193 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 2021-12-03 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) Rrim 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 2.35 50 92.8 0.193 0.932 6.3 17.5 13448
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 2.35 2.39 77.1 0.661 0.691 0.19 0.889 9.1
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 2.36 37.57 12750 698 92.46 0.1707 0.16765 0.1739 0.22562 0.2296 RANDOM 48.487
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] 5.18 -1.87 -3.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.605 r_dihedral_angle_4_deg 23.562 r_dihedral_angle_3_deg 17.257 r_long_range_B_refined 9.793 r_long_range_B_other 9.67 r_dihedral_angle_1_deg 7.406 r_scangle_other 7.173 r_mcangle_other 5.304 r_mcangle_it 5.301 r_scbond_it 4.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.605 r_dihedral_angle_4_deg 23.562 r_dihedral_angle_3_deg 17.257 r_long_range_B_refined 9.793 r_long_range_B_other 9.67 r_dihedral_angle_1_deg 7.406 r_scangle_other 7.173 r_mcangle_other 5.304 r_mcangle_it 5.301 r_scbond_it 4.62 r_scbond_other 4.5 r_mcbond_it 3.424 r_mcbond_other 3.396 r_angle_refined_deg 1.672 r_angle_other_deg 1.308 r_chiral_restr 0.116 r_bond_refined_d 0.007 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 1758 Nucleic Acid Atoms Solvent Atoms 115 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling DENZO data reduction PHASER phasing