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Crystal structure of phosphorylated RET V804M tyrosine kinase domain complexed with PDD00018366
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IVS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.1 M sodium citrate pH 4.5-5.5,
2.0 M sodium formate
drop size 500 nl + 500 nl
RET at 3 mg/ml in 20 mM Tris pH 8.0, 100 mM NaCl, 1 mM DTT
Crystal Properties Matthews coefficient Solvent content 2.72 54.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.38 α = 90 b = 70.04 β = 102.22 c = 78.73 γ = 90
Symmetry Space Group C 1 2 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-F 2016-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97949 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.88 49.77 98.8 0.159 0.175 0.994 4.9 5.7 30797
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.88 1.93 82.7 0.337 0.7 3.6
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 MOLECULAR REPLACEMENT THROUGHOUT 2IVS 1.88 45 29257 1539 98.76 0.20832 0.20677 0.2173 0.23835 0.2476 RANDOM 42.439
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] 1.35 1.12 0.28 -1.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.29 r_dihedral_angle_4_deg 18.241 r_dihedral_angle_3_deg 16.059 r_long_range_B_refined 6.756 r_long_range_B_other 6.738 r_dihedral_angle_1_deg 5.972 r_scangle_other 4.337 r_mcangle_it 3.451 r_mcangle_other 3.451 r_scbond_it 2.638
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.29 r_dihedral_angle_4_deg 18.241 r_dihedral_angle_3_deg 16.059 r_long_range_B_refined 6.756 r_long_range_B_other 6.738 r_dihedral_angle_1_deg 5.972 r_scangle_other 4.337 r_mcangle_it 3.451 r_mcangle_other 3.451 r_scbond_it 2.638 r_scbond_other 2.611 r_mcbond_it 2.147 r_mcbond_other 2.146 r_angle_refined_deg 1.271 r_angle_other_deg 1.131 r_chiral_restr 0.053 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2361 Nucleic Acid Atoms Solvent Atoms 89 Heterogen Atoms 71
Software Software Software Name Purpose GDA data collection XDS data reduction XSCALE data scaling PHASER phasing REFMAC refinement