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Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with AMPPNP at pH 7.0
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 AMPPNP, 2 mM CdCl2, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.75 55.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.134 α = 90 b = 110.504 β = 90 c = 41.437 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 1.8 50 96 0.062 35.1 7.1 37444 -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 1.8 1.83 66.9 0.323 2.9 3.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.8 38.8 34990 2275 95.5 0.20778 0.20596 0.2046 0.23566 0.2331 Equivalent and expanded 26.156
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] -0.17 1.26 -1.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.756 r_dihedral_angle_3_deg 12.318 r_dihedral_angle_4_deg 12.289 r_dihedral_angle_1_deg 5.277 r_scangle_it 3.058 r_scbond_it 1.816 r_mcangle_it 1.312 r_angle_refined_deg 1.261 r_mcbond_it 0.701 r_chiral_restr 0.082
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.756 r_dihedral_angle_3_deg 12.318 r_dihedral_angle_4_deg 12.289 r_dihedral_angle_1_deg 5.277 r_scangle_it 3.058 r_scbond_it 1.816 r_mcangle_it 1.312 r_angle_refined_deg 1.261 r_mcbond_it 0.701 r_chiral_restr 0.082 r_bond_refined_d 0.01 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2547 Nucleic Acid Atoms Solvent Atoms 376 Heterogen Atoms 37
Software Software Software Name Purpose HKL-2000 data collection PHENIX model building REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing