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Crystal structure of TrkA (G595R) kinase domain
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 2.92 57.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.423 α = 90 b = 105.423 β = 90 c = 203.741 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 EIGER X 16M 2019-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.97918 SSRF BL17U1
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 2.55 50 100 0.071 38.25 13.1 14516
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 2.55 2.59 0.456
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 2.55 41.69 13783 724 99.9 0.20184 0.19893 0.202 0.25717 0.2519 RANDOM 60.159
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] 1.62 0.81 1.62 -5.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.938 r_dihedral_angle_4_deg 21.586 r_dihedral_angle_3_deg 21.399 r_long_range_B_other 12.007 r_long_range_B_refined 12.004 r_scangle_other 8.712 r_mcangle_other 8.07 r_mcangle_it 8.055 r_dihedral_angle_1_deg 7.253 r_scbond_it 5.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.938 r_dihedral_angle_4_deg 21.586 r_dihedral_angle_3_deg 21.399 r_long_range_B_other 12.007 r_long_range_B_refined 12.004 r_scangle_other 8.712 r_mcangle_other 8.07 r_mcangle_it 8.055 r_dihedral_angle_1_deg 7.253 r_scbond_it 5.51 r_scbond_other 5.508 r_mcbond_it 5.343 r_mcbond_other 5.284 r_angle_refined_deg 1.539 r_angle_other_deg 1.283 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 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 2401 Nucleic Acid Atoms Solvent Atoms 53 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing