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A pharmacological map of the PI3-K family defines a role for p110 alpha in signaling: The structure of complex of phosphoinositide 3- kinase gamma with inhibitor PIK-39
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 = 143.804 α = 90 b = 67.523 β = 95.45 c = 106.311 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 62.14 99.9 0.06 17.72 3.68 31445 -3.7
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 2.74 100 0.45 2.15 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 62.14 30150 1295 99.8 0.24 0.237 0.2919 0.299 0.3476 RANDOM 62.69
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] -1.28 -0.52 1.87 -0.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.485 r_dihedral_angle_3_deg 20.775 r_dihedral_angle_4_deg 17.625 r_dihedral_angle_1_deg 6.724 r_scangle_it 2.015 r_angle_refined_deg 1.419 r_scbond_it 1.286 r_mcangle_it 0.984 r_mcbond_it 0.562 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.485 r_dihedral_angle_3_deg 20.775 r_dihedral_angle_4_deg 17.625 r_dihedral_angle_1_deg 6.724 r_scangle_it 2.015 r_angle_refined_deg 1.419 r_scbond_it 1.286 r_mcangle_it 0.984 r_mcbond_it 0.562 r_nbtor_refined 0.311 r_nbd_refined 0.242 r_symmetry_vdw_refined 0.212 r_symmetry_hbond_refined 0.188 r_xyhbond_nbd_refined 0.172 r_chiral_restr 0.096 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 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 6807 Nucleic Acid Atoms Solvent Atoms 8 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling TRUNCATE data scaling AMoRE phasing