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Crystal Structures of Pan-PI3-Kinase and Dual Pan-PI3-Kinase/mTOR Inhibitors
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1E8X PDB ENTRY 1E8X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 289 PEG 3350, 0.2M NH4SO4, 0.1M Tris-HCl 8.5, vapor diffusion, hanging drop, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.37 48.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.359 α = 90 b = 67.741 β = 95.63 c = 107.151 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 CCD ADSC QUANTUM 315 2006-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.0 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 3 50 99.9 0.061 14.2 3.9 21245
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 3 3.11 100 0.441 4 2133
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 1E8X 3 20 20813 1064 99.87 0.233 0.23 0.2193 0.275 0.2603 RANDOM 40.652
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] -1.01 2.1 3.14 -1.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.373 r_scangle_it 2.831 r_mcangle_it 2.79 r_mcbond_it 1.778 r_scbond_it 1.763 r_angle_refined_deg 1.187 r_angle_other_deg 0.82 r_nbd_other 0.206 r_nbd_refined 0.194 r_xyhbond_nbd_refined 0.167
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.373 r_scangle_it 2.831 r_mcangle_it 2.79 r_mcbond_it 1.778 r_scbond_it 1.763 r_angle_refined_deg 1.187 r_angle_other_deg 0.82 r_nbd_other 0.206 r_nbd_refined 0.194 r_xyhbond_nbd_refined 0.167 r_symmetry_vdw_other 0.16 r_symmetry_vdw_refined 0.142 r_nbtor_other 0.118 r_chiral_restr 0.064 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6812 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 34
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction