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Crystal structure of human PI3K-gamma in complex with benzimidazole inhibitor 5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WWP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.3 298 20% PEG 3350, 0.1 M Tris (pH 7.3), 0.25 M ammonium sulfate, 2 mM DTT
Crystal Properties Matthews coefficient Solvent content 2.38 48.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.301 α = 90 b = 68.234 β = 95.12 c = 106.62 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 2009-09-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.9793 CLSI 08ID-1
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 2.8 50 99.2 0.07 12.9 3.3 25882 -3 84.3
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 2.8 2.9 99.8 0.552 3.2 2588
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 MOLECULAR REPLACEMENT THROUGHOUT 4WWP 2.8 40 23706 1834 99.18 0.2124 0.2077 0.2088 0.2733 0.2771 RANDOM 73.5
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] -4.22 0.6 4.42 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.378 r_dihedral_angle_4_deg 15.475 r_dihedral_angle_3_deg 15.004 r_dihedral_angle_1_deg 5.821 r_angle_refined_deg 1.067 r_angle_other_deg 0.797 r_chiral_restr 0.058 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.378 r_dihedral_angle_4_deg 15.475 r_dihedral_angle_3_deg 15.004 r_dihedral_angle_1_deg 5.821 r_angle_refined_deg 1.067 r_angle_other_deg 0.797 r_chiral_restr 0.058 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6674 Nucleic Acid Atoms Solvent Atoms 15 Heterogen Atoms 47
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction