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Crystal structure of human Proto-oncogene tyrosine-protein kinase receptor Ret in complex with 4-amino-7-(1-methylcyclopropyl)-N-(5-methyl-1H-pyrazol-3-yl)pyrrolo[2,3-d]pyrimidine-5-carboxamide
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293.15 0.20 M LiCl, 0.10 M Na Asetate, pH5.00, 3 M Na Formate, 5 mM MgCl2
Crystal Properties Matthews coefficient Solvent content 2.37 48.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.714 α = 90 b = 80.215 β = 99.4 c = 79.677 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 2018-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.000 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 1.64 78.63 97.5 0.05 0.057 16.67 4.2 75166
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 1.64 1.89 96.8 0.431 0.491 3.84 4.3
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 1.64 78.63 71467 3698 97.55 0.1921 0.1907 0.198 0.2177 0.2208 RANDOM 26.736
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 0.06 -0.29 -1.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.486 r_dihedral_angle_4_deg 16.609 r_dihedral_angle_3_deg 12.574 r_dihedral_angle_1_deg 5.458 r_angle_refined_deg 1.429 r_angle_other_deg 1.202 r_chiral_restr 0.083 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.486 r_dihedral_angle_4_deg 16.609 r_dihedral_angle_3_deg 12.574 r_dihedral_angle_1_deg 5.458 r_angle_refined_deg 1.429 r_angle_other_deg 1.202 r_chiral_restr 0.083 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4503 Nucleic Acid Atoms Solvent Atoms 369 Heterogen Atoms 46
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction