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Crystal structure of Terrestrivirus inositol pyrophosphate kinase in complex with ADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5W2G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 12% PEG8000, 100mM HEPES pH 7.0, 10mM NaH2PO4 and 10% Ethylene Glycol in presence of 5mM ADP and 10mM MgCl2
Crystal Properties Matthews coefficient Solvent content 2.72 54.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.706 α = 90 b = 104.656 β = 90 c = 102.502 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 2021-09-18 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 1.95 50 98.5 0.049 0.057 0.028 1 12.8 3.8 23739
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 99.6 0.739 0.852 0.416 0.629 3.8
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.96 36.92 20981 1106 90.56 0.20035 0.19862 0.2058 0.23214 0.2352 RANDOM 20.381
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] 0.03 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.202 r_dihedral_angle_4_deg 21.114 r_dihedral_angle_3_deg 15.905 r_dihedral_angle_1_deg 6.587 r_long_range_B_refined 5.674 r_long_range_B_other 5.621 r_scangle_other 2.352 r_mcangle_it 2.191 r_mcangle_other 2.19 r_scbond_it 1.369
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.202 r_dihedral_angle_4_deg 21.114 r_dihedral_angle_3_deg 15.905 r_dihedral_angle_1_deg 6.587 r_long_range_B_refined 5.674 r_long_range_B_other 5.621 r_scangle_other 2.352 r_mcangle_it 2.191 r_mcangle_other 2.19 r_scbond_it 1.369 r_scbond_other 1.363 r_angle_refined_deg 1.249 r_angle_other_deg 1.243 r_mcbond_it 1.236 r_mcbond_other 1.236 r_chiral_restr 0.059 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 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 159 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling HKL-2000 data reduction PHASER phasing