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Structure of RET protein tyrosine kinase in complex with selpercatinib
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6NEC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 295 21-30% PEG3350
0.1M Na Citrate pH5.5
Crystal Properties Matthews coefficient Solvent content 2.41 48.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.621 α = 90 b = 79.975 β = 100.09 c = 79.839 γ = 90
Symmetry Space Group P 1 21 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 Rh coated collimator 2019-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL14-1 1.0 SSRL BL14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.05 100 97.8 0.12 0.143 0.077 9.7 3.3 37447 -3 27.09
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.12 97 0.844 1.028 0.578 0.991 1.5 3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 FOURIER SYNTHESIS THROUGHOUT 6NEC 2.06 78.61 35183 1848 95.91 0.199 0.1964 0.1976 0.249 0.25 RANDOM 31.034
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] 1.24 0.01 -0.03 -1.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.748 r_dihedral_angle_4_deg 19.209 r_dihedral_angle_3_deg 15.91 r_dihedral_angle_1_deg 5.033 r_angle_refined_deg 1.285 r_chiral_restr 0.082 r_bond_refined_d 0.008 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4622 Nucleic Acid Atoms Solvent Atoms 146 Heterogen Atoms 93
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing