☰ Navigation Tabs
Crystal structure of TrkB-d5 bound to neurotrophin-4/5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1B98 1B98 (NEUROTROPHIN), 1WWB (TRK) experimental model PDB 1WWB 1B98 (NEUROTROPHIN), 1WWB (TRK)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 10 MG/ML COMPLEX IN 20MM TRIS, 150MM NACL, PH 7.5, 100MM HEPES PH 7.5, 1.5M LISO4
Crystal Properties Matthews coefficient Solvent content 2.7 46.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.372 α = 90 b = 80.406 β = 90 c = 91.318 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 CCD ADSC CCD MIRRORS 2001-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX14.1 SRS PX14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.7 30 99.2 0.084 19.6 5.4 15635 63.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.8 99.9 0.294 3.7 5.4
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 1B98 (NEUROTROPHIN), 1WWB (TRK) 2.7 20 15411 761 99.2 0.218 0.218 0.2101 0.264 0.2531 RANDOM 47.7
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] 0.52 -7.91 7.39
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 26.2 c_scangle_it 3.12 c_scbond_it 2.728 c_mcangle_it 1.997 c_mcbond_it 1.546 c_angle_deg 1.4 c_improper_angle_d 0.75 c_bond_d 0.007 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 26.2 c_scangle_it 3.12 c_scbond_it 2.728 c_mcangle_it 1.997 c_mcbond_it 1.546 c_angle_deg 1.4 c_improper_angle_d 0.75 c_bond_d 0.007 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3419 Nucleic Acid Atoms Solvent Atoms 60 Heterogen Atoms 20
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing