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Crystal Structure of TrkA D5 domain in complex with two different macrocyclic peptides
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WWA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 277 25% v/v ethylene glycol
Crystal Properties Matthews coefficient Solvent content 3.03 59.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.374 α = 90 b = 50.374 β = 90 c = 143.959 γ = 90
Symmetry Space Group P 43 21 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 IMAGE PLATE RIGAKU RAXIS IV++ 2020-05-20 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 2.34 50 99.8 0.044 0.047 0.016 0.978 20.2 9.3 8455
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 2.34 2.42 99.4 0.351 0.372 0.121 0.966 9.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.34 47.55 7979 429 99.95 0.2212 0.21842 0.2253 0.27596 0.2699 RANDOM 28.21
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] 0.4 0.4 -0.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.294 r_dihedral_angle_4_deg 21.083 r_dihedral_angle_3_deg 16.106 r_dihedral_angle_1_deg 6.855 r_long_range_B_refined 4.739 r_long_range_B_other 4.677 r_mcangle_it 2.743 r_mcangle_other 2.741 r_scangle_other 2.679 r_scbond_it 1.739
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.294 r_dihedral_angle_4_deg 21.083 r_dihedral_angle_3_deg 16.106 r_dihedral_angle_1_deg 6.855 r_long_range_B_refined 4.739 r_long_range_B_other 4.677 r_mcangle_it 2.743 r_mcangle_other 2.741 r_scangle_other 2.679 r_scbond_it 1.739 r_scbond_other 1.738 r_mcbond_it 1.607 r_mcbond_other 1.602 r_angle_refined_deg 1.369 r_angle_other_deg 0.752 r_chiral_restr 0.075 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 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 1037 Nucleic Acid Atoms Solvent Atoms 50 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction MOLREP phasing