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Crystal structure of TrkA 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 0.1M citric acid PH 5.0, 8M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.9 57.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.761 α = 90 b = 104.761 β = 90 c = 204.506 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 2019-09-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97934 CLSI 08ID-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 2.9 44.54 99 0.059 8.2 2.8 9735
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 2.9 3.08 0.49
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 2.9 44.58 9242 491 98.61 0.18843 0.18412 0.198 0.26738 0.2675 RANDOM 95.454
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] 2.74 1.37 2.74 -8.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.904 r_dihedral_angle_3_deg 23.845 r_dihedral_angle_4_deg 18.165 r_long_range_B_refined 18.124 r_long_range_B_other 18.12 r_scangle_other 13.625 r_mcangle_it 13.452 r_mcangle_other 13.447 r_scbond_it 9.409 r_mcbond_it 9.134
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.904 r_dihedral_angle_3_deg 23.845 r_dihedral_angle_4_deg 18.165 r_long_range_B_refined 18.124 r_long_range_B_other 18.12 r_scangle_other 13.625 r_mcangle_it 13.452 r_mcangle_other 13.447 r_scbond_it 9.409 r_mcbond_it 9.134 r_mcbond_other 9.131 r_scbond_other 9.039 r_dihedral_angle_1_deg 7.873 r_angle_refined_deg 1.704 r_angle_other_deg 1.259 r_chiral_restr 0.066 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 2363 Nucleic Acid Atoms Solvent Atoms 21 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing