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Crystal structure of PI3K-gamma in complex with triazine-benzimidazole 1
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 2.41 48.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 145.395 α = 90 b = 68.579 β = 94.69 c = 106.501 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 315 2008-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.0000 ALS 5.0.2
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 2.9 30 99.7 0.09 20 3.7 23416 23346 -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) 2.9 3 97 0.383 2.2 3.1
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 2.9 30 21655 1688 99.65 0.2205 0.21681 0.2049 0.2654 0.2511 RANDOM 88.731
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] -3.58 1.16 5.1 -1.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.239 r_dihedral_angle_3_deg 16.675 r_dihedral_angle_4_deg 15.63 r_dihedral_angle_1_deg 5.234 r_scangle_it 1.871 r_scbond_it 1.11 r_mcangle_it 1.054 r_angle_refined_deg 1.032 r_mcbond_it 0.579 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.239 r_dihedral_angle_3_deg 16.675 r_dihedral_angle_4_deg 15.63 r_dihedral_angle_1_deg 5.234 r_scangle_it 1.871 r_scbond_it 1.11 r_mcangle_it 1.054 r_angle_refined_deg 1.032 r_mcbond_it 0.579 r_nbtor_refined 0.301 r_nbd_refined 0.191 r_symmetry_vdw_refined 0.152 r_symmetry_hbond_refined 0.138 r_xyhbond_nbd_refined 0.127 r_chiral_restr 0.068 r_bond_refined_d 0.009 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 6773 Nucleic Acid Atoms Solvent Atoms 13 Heterogen Atoms 42
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction EPMR phasing