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c-KIT kinase domain in complex with (R)-Pyrrolidine derivative of AZD7762
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8PQ9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 293.15K, 1.5 M Na3-Citrat, 100 mM HEPES, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.38 48.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.82 α = 90 b = 56.82 β = 90 c = 189.66 γ = 120
Symmetry Space Group P 31 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 PIXEL DECTRIS EIGER X 16M 2022-07-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9998989320294075 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) CC (Half) 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 2.1 49.21 100 0.0088 1 19.86 19.8 21603
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.2 100 1.351 0.875
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.1 49.21 2.43 21603 1081 100 0.1858 0.1832 0.1847 0.1995 0.1989 57.28
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 f_dihedral_angle_d 13.328 f_angle_d 0.553 f_chiral_restr 0.0407 f_plane_restr 0.004 f_bond_d 0.0031
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2308 Nucleic Acid Atoms Solvent Atoms 56 Heterogen Atoms 24
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing