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Crystal Structure of phosphorylated RET tyrosine kinase domain with inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IVT PDB ENTRY 2IVT, FLEXIBLE LOOPS REMOVED
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 PROTEIN 4.5 MG/ML IN 20 MM TRIS-HCL PH 8, 100MM NACL,1MM DTT, 1MM EDTA RESERVOIR 1.85 M SODIUM FORMATE, 0.1 SODIUM CITRATE PH 5.5, 0.2M LITHIUM CHLORIDE VAPOUR DIFFUSION, SITTING DROP, 289 K
Crystal Properties Matthews coefficient Solvent content 2.9 57.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.6 α = 90 b = 70.912 β = 101.68 c = 78.871 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 2007-07-29 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 2.6 21.64 99.1 0.06 17 3.1 11886
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 2.6 2.74 100 0.23 5.2 3
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 PDB ENTRY 2IVT, FLEXIBLE LOOPS REMOVED 2.6 30 11316 569 98.9 0.194 0.191 0.256 RANDOM 39.5
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] 0.04 0.32 0.69 -0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.201 r_dihedral_angle_4_deg 22.424 r_dihedral_angle_3_deg 16.325 r_dihedral_angle_1_deg 5.375 r_scangle_it 2.871 r_scbond_it 1.825 r_angle_refined_deg 1.632 r_mcangle_it 1.387 r_mcbond_it 0.774 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.201 r_dihedral_angle_4_deg 22.424 r_dihedral_angle_3_deg 16.325 r_dihedral_angle_1_deg 5.375 r_scangle_it 2.871 r_scbond_it 1.825 r_angle_refined_deg 1.632 r_mcangle_it 1.387 r_mcbond_it 0.774 r_nbtor_refined 0.305 r_nbd_refined 0.205 r_symmetry_vdw_refined 0.196 r_xyhbond_nbd_refined 0.104 r_chiral_restr 0.099 r_symmetry_hbond_refined 0.043 r_bond_refined_d 0.016 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 2234 Nucleic Acid Atoms Solvent Atoms 28 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing