☰ Navigation Tabs
Crystal structure of Terrestrivirus inositol pyrophosphate kinase in complex with AMP-PNP
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 AMP-PNP and 2mM CdCl2
Crystal Properties Matthews coefficient Solvent content 2.77 55.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.489 α = 90 b = 103.417 β = 90 c = 102.669 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 2021-12-19 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 2.59 50 99.5 0.101 0.109 0.04 0.996 8.9 7.1 10740
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 2.59 2.64 100 0.913 0.984 0.361 0.784 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 2.59 37.27 9632 528 94.02 0.18037 0.17763 0.1856 0.22881 0.2471 RANDOM 38.179
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 0.04 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.972 r_dihedral_angle_4_deg 30.742 r_dihedral_angle_3_deg 19.133 r_long_range_B_refined 10.948 r_long_range_B_other 10.527 r_dihedral_angle_1_deg 8.12 r_scangle_other 6.264 r_mcangle_it 5.636 r_mcangle_other 5.636 r_scbond_it 4.068
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.972 r_dihedral_angle_4_deg 30.742 r_dihedral_angle_3_deg 19.133 r_long_range_B_refined 10.948 r_long_range_B_other 10.527 r_dihedral_angle_1_deg 8.12 r_scangle_other 6.264 r_mcangle_it 5.636 r_mcangle_other 5.636 r_scbond_it 4.068 r_scbond_other 3.832 r_mcbond_it 3.466 r_mcbond_other 3.454 r_angle_refined_deg 1.62 r_angle_other_deg 1.277 r_chiral_restr 0.064 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 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 73 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling HKL-2000 data reduction PHASER phasing