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A pharmacological map of the PI3-K family defines a role for p110alpha in signaling: The structure of complex of phosphoinositide 3-kinase gamma with inhibitor PIK-93
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1E8Z PDB ENTRY 1E8Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 VAPOUR DIFFUSION 1 MICROLITER PROTEIN PLUS 1 MICROLITER RESERVOIR RESERVOIR: 17% PEG 4000, 250 MM AMMONIUM SULFATE AND 100 MM TRIS PH 7.5 PROTEIN: 4 MG/ML IN 0.5 MM AMMONIUM SULFATE, 20 MM TRIS PH 7.2, 1% ETHYLENE GLYCOL, 0.02% CHAPS AND 5 MM DTT
Crystal Properties Matthews coefficient Solvent content 2.4 40
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.025 α = 90 b = 68.114 β = 95.21 c = 106.351 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 CCD TORROIDAL MIRROR 2005-01-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 2.6 71.8 99.8 0.07 14.3 3.7 31614 -3.7 70
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 2.6 2.74 99.8 0.36 2.7 3.7
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 1E8Z 2.6 71.8 30445 1306 99.8 0.246 0.244 0.2797 0.302 0.3352 RANDOM 60.68
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] -1.48 1.48 1.84 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.91 r_dihedral_angle_3_deg 19.467 r_dihedral_angle_4_deg 18.131 r_dihedral_angle_1_deg 5.921 r_scangle_it 1.494 r_angle_refined_deg 1.212 r_scbond_it 0.901 r_mcangle_it 0.789 r_mcbond_it 0.45 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.91 r_dihedral_angle_3_deg 19.467 r_dihedral_angle_4_deg 18.131 r_dihedral_angle_1_deg 5.921 r_scangle_it 1.494 r_angle_refined_deg 1.212 r_scbond_it 0.901 r_mcangle_it 0.789 r_mcbond_it 0.45 r_nbtor_refined 0.306 r_nbd_refined 0.223 r_symmetry_vdw_refined 0.168 r_xyhbond_nbd_refined 0.157 r_chiral_restr 0.079 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_symmetry_hbond_refined 0.001 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6802 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling TRUNCATE data scaling AMoRE phasing