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Crystal structure of TrkA (G595R) kinase with repotrectinib
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4YNE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 3.0M NaCl, 0.1M Bis-Tris pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.94 58.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.417 α = 90 b = 105.417 β = 90 c = 204.988 γ = 120
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 PILATUS3 6M 2019-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.9793 SSRF BL18U1
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 2.7 19.94 90.9 0.048 10.5 3.3 11040
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 2.7 2.83 0.478
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4yne 2.7 19.95 10507 533 89.41 0.18594 0.18239 0.1898 0.25615 0.2618 RANDOM 78.034
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] 2.18 1.09 2.18 -7.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.378 r_dihedral_angle_3_deg 22.169 r_dihedral_angle_4_deg 20.566 r_long_range_B_refined 15.185 r_long_range_B_other 15.179 r_mcangle_it 10.551 r_mcangle_other 10.548 r_scangle_other 10.44 r_scbond_it 7.083 r_scbond_other 6.917
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.378 r_dihedral_angle_3_deg 22.169 r_dihedral_angle_4_deg 20.566 r_long_range_B_refined 15.185 r_long_range_B_other 15.179 r_mcangle_it 10.551 r_mcangle_other 10.548 r_scangle_other 10.44 r_scbond_it 7.083 r_scbond_other 6.917 r_mcbond_it 6.912 r_mcbond_other 6.909 r_dihedral_angle_1_deg 6.853 r_angle_refined_deg 1.517 r_angle_other_deg 1.262 r_chiral_restr 0.064 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.002 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 2371 Nucleic Acid Atoms Solvent Atoms 16 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing