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Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with ADP at pH 5.2
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 7 277 12% (w/v) PEG 3350, 20 mM MgCl2, 0.1 M HEPES, 1 mM ATP, 2 mM CdCl2
Soaking under pH5.2 overnight
, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.71 54.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.973 α = 90 b = 110.807 β = 90 c = 41.381 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 300 mm CCD 2011-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
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 1.7 50 99.2 0.057 28.5 5.3 45377 -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 1.7 1.73 94.8 0.423 3 4
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 (All) 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 1.7 41.28 42377 2802 98.72 0.18095 0.18095 0.17927 0.1781 0.20635 0.2035 Equivalent and expanded 17.327
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] 0.5 -0.34 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.997 r_dihedral_angle_4_deg 14.301 r_dihedral_angle_3_deg 11.293 r_dihedral_angle_1_deg 5.429 r_scangle_it 3.498 r_scbond_it 2.066 r_mcangle_it 1.376 r_angle_refined_deg 1.189 r_mcbond_it 0.719 r_chiral_restr 0.084
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.997 r_dihedral_angle_4_deg 14.301 r_dihedral_angle_3_deg 11.293 r_dihedral_angle_1_deg 5.429 r_scangle_it 3.498 r_scbond_it 2.066 r_mcangle_it 1.376 r_angle_refined_deg 1.189 r_mcbond_it 0.719 r_chiral_restr 0.084 r_bond_refined_d 0.01 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2558 Nucleic Acid Atoms Solvent Atoms 431 Heterogen Atoms 62
Software Software Software Name Purpose HKL-2000 data collection PHENIX model building REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing