8PPF

Human inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic domain in complex with beta-D-glucopyranosyl 1,3,4-trisphosphate/AMP-PNP/Mg


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1W2CChain A

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52910.81 M sodium citrate, 0.1M Tris pH 8.5 and 0.1 M NaCl. Protein:precipitant ratio 1:1. Protein concentration: 18 mg/ml. Protein buffer: 20 mM Tris pH 7.5, 50 mM ammonium sulfate and 2 mM DTT. Soaking 2h with 1.5 M lithium sulfate, 0.1 M Tris pH 8.5, 5 mM ligand, 3 mM AMP-PNP and 3 mM MgCl2.
Crystal Properties
Matthews coefficientSolvent content
2.7154.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.815α = 90
b = 97.587β = 90
c = 191.929γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MKB mirrors, rectangular beam shape2021-06-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.979264ALBAXALOC

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.8548.8496.80.040.9941210.55671429.545
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.851.8974.30.2630.7792.27.2

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 SYNTHESISTHROUGHOUT1.8548.8453680298696.630.197350.195630.22779RANDOM42.004
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]
0.820.61-1.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg25.943
r_dihedral_angle_4_deg16.653
r_dihedral_angle_3_deg16.578
r_long_range_B_refined7.243
r_long_range_B_other7.179
r_dihedral_angle_1_deg6.343
r_scangle_other4.73
r_mcangle_other3.872
r_mcangle_it3.87
r_scbond_it2.932
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg25.943
r_dihedral_angle_4_deg16.653
r_dihedral_angle_3_deg16.578
r_long_range_B_refined7.243
r_long_range_B_other7.179
r_dihedral_angle_1_deg6.343
r_scangle_other4.73
r_mcangle_other3.872
r_mcangle_it3.87
r_scbond_it2.932
r_scbond_other2.89
r_mcbond_it2.506
r_mcbond_other2.499
r_angle_refined_deg1.356
r_angle_other_deg1.256
r_chiral_restr0.064
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 Atoms4355
Nucleic Acid Atoms
Solvent Atoms364
Heterogen Atoms140

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
REFMACphasing
Cootmodel building
PDB_EXTRACTdata extraction