8PPI

Human inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic domain in complex with beta-D-glucopyranosylmethanol 3,4,1'-trisphosphate/ATP/Mn


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 ATP and 3 mM MnCl2.
Crystal Properties
Matthews coefficientSolvent content
2.7955.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.953α = 90
b = 98.124β = 90
c = 193.163γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 2MKB mirror, elliptical beam shape2021-10-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.873128ESRFID23-2

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
11.65193.1691.90.0240.99915.512.87785025.115
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)
11.651.681000.4930.621.711.6

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 SYNTHESISTHROUGHOUT1.6596.5873888389291.950.186360.184880.21405RANDOM35.226
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]
0.560.21-0.78
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg25.081
r_dihedral_angle_4_deg15.978
r_dihedral_angle_3_deg15.213
r_long_range_B_refined7.051
r_long_range_B_other6.939
r_dihedral_angle_1_deg6.161
r_scangle_other4.361
r_mcangle_other3.41
r_mcangle_it3.409
r_scbond_it2.774
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg25.081
r_dihedral_angle_4_deg15.978
r_dihedral_angle_3_deg15.213
r_long_range_B_refined7.051
r_long_range_B_other6.939
r_dihedral_angle_1_deg6.161
r_scangle_other4.361
r_mcangle_other3.41
r_mcangle_it3.409
r_scbond_it2.774
r_scbond_other2.74
r_mcbond_it2.134
r_mcbond_other2.128
r_angle_refined_deg1.379
r_angle_other_deg1.26
r_chiral_restr0.063
r_gen_planes_refined0.006
r_bond_refined_d0.005
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 Atoms4403
Nucleic Acid Atoms
Solvent Atoms473
Heterogen Atoms149

Software

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