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Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with ADP and 1,5-(PCP)2-IP4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3T7A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 12% (w/v) PEG 3350, 20 mM MgCl2, 0.1 M HEPES, pH 7.0, 1 mM ATP and 2 mM CdCl2. The crystals were transferred to a stabilizing buffer containing 22% (w/v) PEG 3350, 10 mM MgCl2, 0.1 M sodium acetate, pH 5.2 at 4 oC overnight, while ATP in the crystals was hydrolyzed to ADP. The crystals were soaked under the above stabilizing buffer for three days with 2 mM analog.
Crystal Properties Matthews coefficient Solvent content 2.79 55.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.567 α = 90 b = 110.4 β = 90 c = 41.455 γ = 90
Symmetry Space Group P 21 21 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 CCD MARMOSAIC 225 mm CCD 2015-04-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.0 APS 22-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 1.9 50 99.9 0.113 15.76 6.6 32965
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.93 99.9 0.668 2.42 6.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 FOURIER SYNTHESIS THROUGHOUT 3T7A 1.9 35.57 30891 2017 99.76 0.1448 0.1413 0.1416 0.199 0.1985 Equivalent 22.557
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] 0.6 -0.3 -0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.375 r_sphericity_free 33.36 r_dihedral_angle_4_deg 13.155 r_sphericity_bonded 13.065 r_dihedral_angle_3_deg 12.461 r_dihedral_angle_1_deg 5.264 r_mcangle_it 2.514 r_scbond_it 2.249 r_rigid_bond_restr 2.096 r_mcbond_it 1.834
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.375 r_sphericity_free 33.36 r_dihedral_angle_4_deg 13.155 r_sphericity_bonded 13.065 r_dihedral_angle_3_deg 12.461 r_dihedral_angle_1_deg 5.264 r_mcangle_it 2.514 r_scbond_it 2.249 r_rigid_bond_restr 2.096 r_mcbond_it 1.834 r_angle_refined_deg 1.327 r_chiral_restr 0.107 r_bond_refined_d 0.007 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2550 Nucleic Acid Atoms Solvent Atoms 445 Heterogen Atoms 112
Software Software Software Name Purpose HKL-2000 data reduction HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing