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Crystal structure of phosphorylated RET tyrosine kinase domain complexed with a pyrrolo[2,3-d]pyrimidine inhibitor.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6VHG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 294 1.8M Ammonium sulfate, 0.1M sodium acetate pH 4.6
Crystal Properties Matthews coefficient Solvent content 2.61 52.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.131 α = 90 b = 98.131 β = 90 c = 145.381 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2014-01-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 0.97648 ALS 5.0.3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim 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 3.5 50 100 0.127 0.166 0.051 0.996 13.1 5.7 10093 59.68
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.5 3.63 100 0.494 0.576 1.76 5.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6VHG 3.51 49.07 1.38 8985 475 89.98 0.2219 0.2202 0.2469 0.2833 62.98
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 16.1892 f_angle_d 0.6491 f_chiral_restr 0.044 f_plane_restr 0.0037 f_bond_d 0.0022
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4545 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 64
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction SCALEPACK data scaling REFMAC phasing