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Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with AMPPNP and inositol hexakisphosphate (IP6)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3T54 PDB ENTRY 3T54
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 12% (w/v) PEG 3350, 20 mM MgCl2, 0.1 M HEPES, pH 7.0, 1 mM AMPPNP, 2 mM CdCl2, Soaking with 10mM IP6 and 10 mM NaF under pH 5.2 for 3 days, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.71 54.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.037 α = 90 b = 110.489 β = 90 c = 41.339 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 RIGAKU SATURN 92 2011-03-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 99.7 0.062 26.1 6.1 32957 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.93 77.4 0.362 3.1 3.2
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 PDB ENTRY 3T54 1.9 23.55 30739 2005 99.25 0.18719 0.18524 0.1861 0.21707 0.2165 Equivalent and expanded 19.473
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] 0.22 -0.11 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.441 r_dihedral_angle_4_deg 15.041 r_dihedral_angle_3_deg 13.304 r_dihedral_angle_1_deg 5.583 r_scangle_it 3.13 r_scbond_it 1.906 r_angle_refined_deg 1.335 r_mcangle_it 1.31 r_mcbond_it 0.702 r_chiral_restr 0.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.441 r_dihedral_angle_4_deg 15.041 r_dihedral_angle_3_deg 13.304 r_dihedral_angle_1_deg 5.583 r_scangle_it 3.13 r_scbond_it 1.906 r_angle_refined_deg 1.335 r_mcangle_it 1.31 r_mcbond_it 0.702 r_chiral_restr 0.085 r_bond_refined_d 0.011 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2604 Nucleic Acid Atoms Solvent Atoms 424 Heterogen Atoms 71
Software Software Software Name Purpose HKL-2000 data collection PHENIX model building REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing