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c-KIT kinase domain in complex with IDRX-42 via soaking
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6GQK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 first: co-crystallization of crenolanib (2 mg/mL, 100 mM HEPES, pH 8.0), second: for soaking of IDRX-42: evaporation of 10 mM IDRX-42 in DMSO, resolve to 20 mM DMSO, set drop next to crystallization drop, connect drops, incubate 24 hrs
Crystal Properties Matthews coefficient Solvent content 2.25 36.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.74 α = 90 b = 59.29 β = 90 c = 192.46 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 2 1 x-ray 100 PIXEL DECTRIS EIGER2 X 9M 2023-09-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 2 SYNCHROTRON ESRF BEAMLINE ID30B 0.91881 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 48.12 99.1 0.998 11.79 5.51 45984 46.29
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2 2 2.1 0.779 1.53
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 48.12 1.34 45939 2297 99.08 0.2042 0.2029 0.2032 0.2311 0.2309 58.8
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 15.8199 f_angle_d 0.4731 f_chiral_restr 0.0389 f_plane_restr 0.0031 f_bond_d 0.0028
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4369 Nucleic Acid Atoms Solvent Atoms 109 Heterogen Atoms 154
Software Software Software Name Purpose PDB_EXTRACT data extraction PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing