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Crystal structure of PI3K-gamma in complex with triazine-benzimidazole 32
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 7.3 298 21% PEG 3350, 0.1 M Tris pH 7.3, 245 mM ammonium sulfate, 5 mM EDTA, VAPOR DIFFUSION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.35 47.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.838 α = 90 b = 68.015 β = 95.45 c = 106.046 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 ADSC QUANTUM 210 2008-10-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.97740 ALS 5.0.1
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 2.65 30 99.7 0.088 19.3 3.7 29831 29742 -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) 2.65 2.74 97 0.414 2 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 (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 PDB ENTRY 1E8Y 2.65 30 27988 1754 99.66 0.23734 0.23383 0.2218 0.29364 0.2763 RANDOM 70.582
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] -3.8 -0.99 4.79 -1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.883 r_dihedral_angle_3_deg 15.865 r_dihedral_angle_4_deg 15.737 r_dihedral_angle_1_deg 5.23 r_scangle_it 1.049 r_angle_refined_deg 0.987 r_scbond_it 0.64 r_mcangle_it 0.603 r_mcbond_it 0.34 r_nbtor_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.883 r_dihedral_angle_3_deg 15.865 r_dihedral_angle_4_deg 15.737 r_dihedral_angle_1_deg 5.23 r_scangle_it 1.049 r_angle_refined_deg 0.987 r_scbond_it 0.64 r_mcangle_it 0.603 r_mcbond_it 0.34 r_nbtor_refined 0.298 r_nbd_refined 0.185 r_xyhbond_nbd_refined 0.129 r_symmetry_vdw_refined 0.106 r_chiral_restr 0.068 r_symmetry_hbond_refined 0.035 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6750 Nucleic Acid Atoms Solvent Atoms 21 Heterogen Atoms 38
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction EPMR phasing