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Crystal structure of the catalytic domain of PPIP5K2 in complex with AMPPNP and 5-PA-InsP5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3T9B PDB ENTRY 3T9B
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 AMPPNP with 2 mM CdCl2 Soaking under 22% PEG3350, 10 mM MgCl2 0.1 M Sodium Acetate, pH5.2 with 10 mM 5PA-InsP5, 3 days, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.75 55.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.623 α = 90 b = 111.226 β = 90 c = 41.443 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 2012-02-23 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 2 50 97.4 0.114 17.4 4.9 28028 28028 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 2 2.03 91.3 0.511 3.2 3 1307
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 3T9B 2 34.28 26130 26130 1698 96.56 0.20027 0.20027 0.19822 0.199 0.23145 0.2326 RANDOM 23.063
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] -0.03 1.12 -1.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.531 r_dihedral_angle_4_deg 15.365 r_dihedral_angle_3_deg 14.112 r_long_range_B_refined 6.407 r_long_range_B_other 5.827 r_dihedral_angle_1_deg 5.199 r_angle_other_deg 3.583 r_scangle_other 2.18 r_scbond_other 1.471 r_scbond_it 1.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.531 r_dihedral_angle_4_deg 15.365 r_dihedral_angle_3_deg 14.112 r_long_range_B_refined 6.407 r_long_range_B_other 5.827 r_dihedral_angle_1_deg 5.199 r_angle_other_deg 3.583 r_scangle_other 2.18 r_scbond_other 1.471 r_scbond_it 1.47 r_angle_refined_deg 1.296 r_mcangle_it 1.212 r_mcangle_other 1.212 r_mcbond_it 0.686 r_mcbond_other 0.686 r_chiral_restr 0.083 r_bond_refined_d 0.01 r_gen_planes_other 0.005 r_gen_planes_refined 0.004 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2604 Nucleic Acid Atoms Solvent Atoms 348 Heterogen Atoms 74
Software Software Software Name Purpose HKL-2000 data collection CCP4 model building REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling CCP4 phasing