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Crystal structure of human Proto-oncogene tyrosine-protein kinase receptor Ret in complex with Pralsetinib
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293.15 0.20 M LiCl, 0.10 M Na Acetate, pH 4.50, 2.5 M Na Formate, 5 mM MgCl2
Crystal Properties Matthews coefficient Solvent content 2.41 48.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.887 α = 90 b = 80.577 β = 99.72 c = 79.866 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 PILATUS 6M 2019-03-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9999 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim 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 2.31 78.72 97.1 0.094 0.119 10.45 2.7 27199
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.31 2.56 97.7 0.44 0.551 2.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MOLECULAR REPLACEMENT THROUGHOUT 2.31 78.72 26013 1185 97.15 0.2204 0.219 0.2235 0.249 0.2431 RANDOM 39.012
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] 1.54 0.15 -0.47 -1.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.635 r_dihedral_angle_4_deg 15.156 r_dihedral_angle_3_deg 14.102 r_dihedral_angle_1_deg 6.315 r_angle_refined_deg 1.551 r_angle_other_deg 1.229 r_chiral_restr 0.082 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.635 r_dihedral_angle_4_deg 15.156 r_dihedral_angle_3_deg 14.102 r_dihedral_angle_1_deg 6.315 r_angle_refined_deg 1.551 r_angle_other_deg 1.229 r_chiral_restr 0.082 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4478 Nucleic Acid Atoms Solvent Atoms 172 Heterogen Atoms 86
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction