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The crystal structure of TrkA kinase in complex with 4^6-methyl-N-(3-(4-methyl-1H-imidazol-1-yl)-5-(trifluoromethyl)phenyl)-11-oxo-5-oxa-10,14-diaza-1(3,6)-imidazo[1,2-b]pyridazina-4(1,3)-benzenacyclotetradecaphan-2-yne-4^5-carboxamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6PMC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289 0.1M Na2HPO4/KH2PO4 (pH 6.2), 2M NaCl
Crystal Properties Matthews coefficient Solvent content 2.64 53.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.125 α = 90 b = 52.125 β = 90 c = 228.168 γ = 120
Symmetry Space Group P 31 1 2
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 RAYONIX MX-300 2022-01-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CAMD BEAMLINE GCPCC 0.978 CAMD GCPCC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3 25.41 99.6 0.991 10.47 10.8 7383 44.1947006656
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.11 0.816
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3.0005 25.4079193508 1.37438196642 7383 736 99.4343434343 0.232612219336 0.22648174138 0.2318 0.289095584517 0.2974 40.3302832716
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.0282976868 f_angle_d 0.790226642506 f_chiral_restr 0.0262545442761 f_plane_restr 0.00347749377958 f_bond_d 0.00331425690791
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2251 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 48
Software Software Software Name Purpose PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing Coot model building