8T8U

Crystal structure of Terrestrivirus full-length Inositol pyrophosphate kinase in complex with ADP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5W2G 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP727712% PEG8000, 100mM HEPES pH 7.0, 10mM NaH2PO4 and 10% Ethylene Glycol in presence of 5mM ADP and 10mM MgCl2
Crystal Properties
Matthews coefficientSolvent content
2.7455.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.929α = 90
b = 104.902β = 90
c = 102.395γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2021-09-18MSINGLE 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
125099.60.0810.0860.0280.9879.89.522385
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)
122.0397.80.8650.9230.3110.7188.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5W2G2.0136.9619768109192.270.175230.173620.20443RANDOM27.321
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]
0.04-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.946
r_dihedral_angle_4_deg28.219
r_dihedral_angle_3_deg15.007
r_dihedral_angle_1_deg6.614
r_long_range_B_refined5.995
r_long_range_B_other5.985
r_scangle_other2.958
r_mcangle_it2.653
r_mcangle_other2.652
r_scbond_it1.745
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.946
r_dihedral_angle_4_deg28.219
r_dihedral_angle_3_deg15.007
r_dihedral_angle_1_deg6.614
r_long_range_B_refined5.995
r_long_range_B_other5.985
r_scangle_other2.958
r_mcangle_it2.653
r_mcangle_other2.652
r_scbond_it1.745
r_scbond_other1.729
r_mcbond_it1.544
r_mcbond_other1.542
r_angle_refined_deg1.243
r_angle_other_deg1.231
r_chiral_restr0.055
r_bond_refined_d0.004
r_gen_planes_refined0.004
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 Atoms1758
Nucleic Acid Atoms
Solvent Atoms168
Heterogen Atoms34

Software

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