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Crystal structure of partially phosphorylated RET V804M tyrosine kinase domain complexed with PDD00018412
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, HANGING 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 2.23 44.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.675 α = 90 b = 80.336 β = 99.87 c = 79.74 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 PIXEL DECTRIS PILATUS 6M-F 2016-02-14 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) 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 2.05 45.89 96.4 0.08 1 7.5 3.1 38208
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.11 75 0.47 0.73 1.3 2.1
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2IVS 2.05 45.89 36312 1876 96.33 0.17871 0.17601 0.22928 0.2174 RANDOM 33.246
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] 2.58 1.11 -1.03 -1.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.956 r_dihedral_angle_4_deg 21.742 r_dihedral_angle_3_deg 16.772 r_long_range_B_refined 7.694 r_long_range_B_other 7.686 r_dihedral_angle_1_deg 6.431 r_scangle_other 5.876 r_mcangle_it 4.217 r_mcangle_other 4.217 r_scbond_it 3.854
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.956 r_dihedral_angle_4_deg 21.742 r_dihedral_angle_3_deg 16.772 r_long_range_B_refined 7.694 r_long_range_B_other 7.686 r_dihedral_angle_1_deg 6.431 r_scangle_other 5.876 r_mcangle_it 4.217 r_mcangle_other 4.217 r_scbond_it 3.854 r_scbond_other 3.808 r_mcbond_other 2.882 r_mcbond_it 2.881 r_angle_refined_deg 1.645 r_angle_other_deg 1.28 r_chiral_restr 0.078 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 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 4569 Nucleic Acid Atoms Solvent Atoms 212 Heterogen Atoms 116
Software Software Software Name Purpose GDA data collection XDS data reduction XDS data scaling PHASER phasing REFMAC refinement