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Crystal Structure of TrkA D5 domain in complex with macrocyclic peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WWA 1WWA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 0.1 M Tris pH 8.5, , 25% w/v Polyethylene glycol 3,350, 0.2 M ammonium acetate
Crystal Properties Matthews coefficient Solvent content 2.69 54.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.68 α = 90 b = 66.972 β = 90 c = 79.889 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ 2018-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.26 50 100 0.055 0.061 0.027 0.998 12.7 5 13490
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.26 2.34 100 0.302 0.34 0.154 0.927 4.7
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 1WWA 2.26 50 12839 609 99.7 0.19891 0.19668 0.2008 0.24947 0.2524 RANDOM 29.8
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] -0.38 0.51 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.221 r_dihedral_angle_4_deg 22.956 r_dihedral_angle_3_deg 15.156 r_dihedral_angle_1_deg 7.225 r_long_range_B_refined 4.02 r_long_range_B_other 3.988 r_mcangle_it 2.582 r_mcangle_other 2.581 r_scangle_other 2.249 r_mcbond_it 1.506
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.221 r_dihedral_angle_4_deg 22.956 r_dihedral_angle_3_deg 15.156 r_dihedral_angle_1_deg 7.225 r_long_range_B_refined 4.02 r_long_range_B_other 3.988 r_mcangle_it 2.582 r_mcangle_other 2.581 r_scangle_other 2.249 r_mcbond_it 1.506 r_mcbond_other 1.504 r_scbond_it 1.416 r_scbond_other 1.415 r_angle_refined_deg 1.235 r_angle_other_deg 0.703 r_chiral_restr 0.071 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 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 1727 Nucleic Acid Atoms Solvent Atoms 91 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction MOLREP phasing