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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 2.53 51.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.999 α = 90 b = 70.685 β = 110.35 c = 71.573 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 CCD ADSC CCD 2007-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 67.12 89.5 0.06 9.09 3.48 20421 30
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 2.11 54.6 0.51 0.79 2.33
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2IVT, FLEXIBLE LOOPS REMOVED 2 20 19337 1055 89.5 0.214 0.211 0.2164 0.269 RANDOM 37.36
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] 0.33 1.69 -0.72 1.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.265 r_dihedral_angle_4_deg 20.383 r_dihedral_angle_3_deg 14.897 r_dihedral_angle_1_deg 5.315 r_scangle_it 3.842 r_scbond_it 2.674 r_angle_refined_deg 1.678 r_mcangle_it 1.668 r_mcbond_it 1.081 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.265 r_dihedral_angle_4_deg 20.383 r_dihedral_angle_3_deg 14.897 r_dihedral_angle_1_deg 5.315 r_scangle_it 3.842 r_scbond_it 2.674 r_angle_refined_deg 1.678 r_mcangle_it 1.668 r_mcbond_it 1.081 r_nbtor_refined 0.313 r_nbd_refined 0.215 r_symmetry_vdw_refined 0.202 r_symmetry_hbond_refined 0.191 r_xyhbond_nbd_refined 0.186 r_chiral_restr 0.109 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 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 2214 Nucleic Acid Atoms Solvent Atoms 71 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing