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Crystal structure of non-phosphorylated RET tyrosine kinase domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GJO PDB ENTRY 1GJO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 PROTEIN 3 MG/ML IN 20 MM TRIS-HCL PH 8.0, 10MM NACL, 1MM DTT RESERVOIR 2.0 M SODIUM FORMATE, 0.1M SODIUM CITRATE PH 5.5 VAPOUR DIFFUSION, SITTING DROP,295 K
Crystal Properties Matthews coefficient Solvent content 2.22 47.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.399 α = 90 b = 80.217 β = 100.09 c = 79.684 γ = 90
Symmetry Space Group P 1 21 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 2003-09-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 27.9 97.5 0.08 16 4 41522
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 2.07 80.6 0.25 10 2
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 1GJO 2 50 39256 2087 97.7 0.183 0.18 0.229 RANDOM 21.26
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] 1.66 0.21 -0.32 -1.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.637 r_dihedral_angle_4_deg 18.987 r_dihedral_angle_3_deg 13.161 r_dihedral_angle_1_deg 5.321 r_scangle_it 3.979 r_scbond_it 2.609 r_mcangle_it 1.661 r_angle_refined_deg 1.52 r_mcbond_it 1.015 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.637 r_dihedral_angle_4_deg 18.987 r_dihedral_angle_3_deg 13.161 r_dihedral_angle_1_deg 5.321 r_scangle_it 3.979 r_scbond_it 2.609 r_mcangle_it 1.661 r_angle_refined_deg 1.52 r_mcbond_it 1.015 r_nbtor_refined 0.306 r_nbd_refined 0.198 r_symmetry_hbond_refined 0.195 r_xyhbond_nbd_refined 0.177 r_symmetry_vdw_refined 0.166 r_chiral_restr 0.105 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 4311 Nucleic Acid Atoms Solvent Atoms 262 Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing