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Crystal structure of phosphorylated RET tyrosine kinase domain complexed with the inhibitor ZD6474
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other IN-HOUSE PART-REFINED STRUCTURE OF RET KINASE DOMAIN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 PROTEIN 3 MG/ML IN 20 MM TRIS-HCL PH 8.0, 100MM NACL, 1MM DTT, 1MM EDTA, 1MM SODIUM VANADATE RESERVOIR 2.2 M SODIUM FORMATE, 0.1M SODIUM ACETATE PH 4.5 VAPOUR DIFFUSION, SITTING DROP, 289 K
Crystal Properties Matthews coefficient Solvent content 2.75 57.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.409 α = 90 b = 71.42 β = 101.23 c = 78.834 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 IMAGE PLATE MARRESEARCH MIRRORS 2005-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.5 15.3 99.6 0.06 9.6 3.7 13506
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.64 99.6 0.16 4.6 3.7
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT IN-HOUSE PART-REFINED STRUCTURE OF RET KINASE DOMAIN 2.5 50 12835 670 99.5 0.193 0.19 0.248 RANDOM 35.62
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] 0.23 0.25 0.2 -0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.199 r_dihedral_angle_4_deg 20.204 r_dihedral_angle_3_deg 15.589 r_dihedral_angle_1_deg 5.924 r_scangle_it 3.368 r_scbond_it 2.279 r_angle_refined_deg 1.614 r_mcangle_it 1.537 r_mcbond_it 0.915 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.199 r_dihedral_angle_4_deg 20.204 r_dihedral_angle_3_deg 15.589 r_dihedral_angle_1_deg 5.924 r_scangle_it 3.368 r_scbond_it 2.279 r_angle_refined_deg 1.614 r_mcangle_it 1.537 r_mcbond_it 0.915 r_nbtor_refined 0.306 r_symmetry_vdw_refined 0.202 r_nbd_refined 0.193 r_xyhbond_nbd_refined 0.154 r_chiral_restr 0.104 r_symmetry_hbond_refined 0.072 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2189 Nucleic Acid Atoms Solvent Atoms 71 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing