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KIT123-KITbp complex (Domains D1-3 of the human receptor tyrosine kinase KIT complexed with the de novo designed minibinder KITbp)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2E9W Only domains D1-3 from the PDB structure were used in silico model AlphaFold Structure generated based on the provided de novo designed protein sequence
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.2 M sodium/potassium phosphate pH 7.5, 0.1 M HEPES pH 7.5, 22.5 % PEG Smear Medium, 10 % glycerol
Crystal Properties Matthews coefficient Solvent content 3.11 60.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.273 α = 90 b = 78.643 β = 90 c = 291.008 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 1 1 x-ray 100 PIXEL DECTRIS EIGER X 16M KB mirrors 2024-05-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9762 PETRA III, EMBL c/o DESY P13 (MX1)
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 2.8 72.75 99.8 0.435 0.99 5.24 10.3 24388 51.56
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 2.8 2.9 99.4 2.639 0.652 0.69 9.7
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.8 72.75 1.34 15528 736 63.58 0.2254 0.2226 0.2219 0.2817 0.2713 Random selection 49.62
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 9.2784 f_angle_d 0.443 f_chiral_restr 0.0417 f_plane_restr 0.0031 f_bond_d 0.0018
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5472 Nucleic Acid Atoms Solvent Atoms 31 Heterogen Atoms 136
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling Coot model building PHASER phasing