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KIT kinase domain mutant D816H in complex with sunitinib
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Sunitinib bound wild-type kinase domain of KIT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 286 1.5 M Ammonium sulfate, 286K, pH 7, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.79 55.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.462 α = 90 b = 101.783 β = 90 c = 105.505 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 98 CCD ADSC QUANTUM 315 Mirrors 2007-09-01 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) R Sym 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 20 99.2 0.042 0.042 4.6 26965 26751 30.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.6 2.69 96.8 0.216 0.216 7.6 4.2 2683
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 Sunitinib bound wild-type kinase domain of KIT 2.6 20 26921 25905 1307 95.9 0.212 0.207 0.204 0.2031 0.255 0.2543 Random
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]
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21 c_angle_deg 0.9 c_improper_angle_d 0.66 c_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4658 Nucleic Acid Atoms Solvent Atoms 15 Heterogen Atoms 49
Software Software Software Name Purpose ADSC data collection CNX refinement HKL-2000 data reduction SCALEPACK data scaling CNX phasing