8T8Y

Crystal structure of Terrestrivirus inositol pyrophosphate kinase in complex with ADP and 1,4,5-InsP3


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP727712% 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 myo-1,4,5-IP3, 5mM ADP and 10mM MgCl2
Crystal Properties
Matthews coefficientSolvent content
2.8156.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.619α = 90
b = 100.61β = 90
c = 105.022γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2021-12-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.0APS22-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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.550990.1420.1520.0540.978.5812033
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)RedundancyNumber Unique Reflections (All)
12.52.541000.8380.8940.3080.8648.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT2.537.81124560697.360.175930.173340.22339RANDOM36.217
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]
0.02-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.763
r_dihedral_angle_4_deg23.946
r_dihedral_angle_3_deg17.274
r_dihedral_angle_1_deg7.419
r_long_range_B_refined7.125
r_long_range_B_other7.124
r_scangle_other4.179
r_mcangle_it3.894
r_mcangle_other3.894
r_scbond_other2.466
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.763
r_dihedral_angle_4_deg23.946
r_dihedral_angle_3_deg17.274
r_dihedral_angle_1_deg7.419
r_long_range_B_refined7.125
r_long_range_B_other7.124
r_scangle_other4.179
r_mcangle_it3.894
r_mcangle_other3.894
r_scbond_other2.466
r_scbond_it2.463
r_mcbond_it2.301
r_mcbond_other2.259
r_angle_refined_deg1.442
r_angle_other_deg1.218
r_chiral_restr0.106
r_bond_refined_d0.005
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms1764
Nucleic Acid Atoms
Solvent Atoms117
Heterogen Atoms53

Software

Software
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
HKL-2000data reduction
PHASERphasing