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Crystal structure of human PI3K-gamma in complex with a pyridyl-triazine inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1E8Y PDB entry 1E8Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.3 273 21% polyethylene glycol 3350, 100 mM Tris, 245 mM ammonium sulfate, 1 mM DTT, 2 mM EDTA, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 273K
Crystal Properties Matthews coefficient Solvent content 2.39 48.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.775 α = 90 b = 68.233 β = 94.99 c = 107.182 γ = 90
Symmetry Space Group C 1 2 1
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 2009-02-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.0000 APS 22-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.95 50 99.8 0.075 10.1 3.4 22189 22145 -3
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 2.95 3.06 99.6 0.737 3.3 2186
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1E8Y 2.95 50 22050 21966 1584 99.62 0.2239 0.2188 0.2891 0.2764 RANDOM 87.3493
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] -1.85 0.77 2.85 -0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.758 r_dihedral_angle_3_deg 17.067 r_dihedral_angle_4_deg 15.327 r_dihedral_angle_1_deg 5.167 r_scangle_it 1.071 r_angle_refined_deg 1.002 r_mcangle_it 0.937 r_scbond_it 0.657 r_mcbond_it 0.521 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.758 r_dihedral_angle_3_deg 17.067 r_dihedral_angle_4_deg 15.327 r_dihedral_angle_1_deg 5.167 r_scangle_it 1.071 r_angle_refined_deg 1.002 r_mcangle_it 0.937 r_scbond_it 0.657 r_mcbond_it 0.521 r_nbtor_refined 0.302 r_nbd_refined 0.194 r_xyhbond_nbd_refined 0.133 r_symmetry_vdw_refined 0.127 r_symmetry_hbond_refined 0.068 r_chiral_restr 0.067 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6757 Nucleic Acid Atoms Solvent Atoms 14 Heterogen Atoms 49
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling EPMR phasing