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Targeted polypharmacology: crystal structure of the c-Src kinase domain in complex with S1, a multitargeted kinase inhibitor
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 16 mg/mL kinase, 50 mM Tris-HCl, 100 mM NaCl, 5% (v/v) glycerol mixed 1:1 with 18% (w/v) glycerol precipitant well solution, pH 8.0, vapor diffusion, hanging drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.97 58.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.429 α = 100.84 b = 62.984 β = 91.81 c = 74.028 γ = 89.61
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 2007-07-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 1.000 ALS 8.2.2
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 2.8 50 98.8 0.124 11.763 3.8 18046
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 2.8 2.9 98.2 0.497 3.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.81 37.13 17102 924 98.4 0.20921 0.20661 0.2574 0.2421 RANDOM 14.27
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] -0.03 -0.01 0.02 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.216 r_dihedral_angle_4_deg 17.313 r_dihedral_angle_3_deg 16.467 r_dihedral_angle_1_deg 6.325 r_scangle_it 2.828 r_scbond_it 1.714 r_angle_refined_deg 1.538 r_mcangle_it 0.931 r_mcbond_it 0.477 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.216 r_dihedral_angle_4_deg 17.313 r_dihedral_angle_3_deg 16.467 r_dihedral_angle_1_deg 6.325 r_scangle_it 2.828 r_scbond_it 1.714 r_angle_refined_deg 1.538 r_mcangle_it 0.931 r_mcbond_it 0.477 r_nbtor_refined 0.301 r_symmetry_vdw_refined 0.196 r_nbd_refined 0.192 r_xyhbond_nbd_refined 0.131 r_symmetry_hbond_refined 0.131 r_chiral_restr 0.092 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 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 3774 Nucleic Acid Atoms Solvent Atoms 6 Heterogen Atoms 20
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling