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Crystal structure of N-terminal fragment of Zebrafish Toll-Like Receptor 5 (TLR5) with Lamprey Variable Lymphocyte Receptor 9 (VLR9) bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3V47
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 15% Peg3350, 170 mM MgNO3, 80 mM MES pH 6.0, 15% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.57 52.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.38 α = 112.14 b = 69.413 β = 104.12 c = 84.561 γ = 100.81
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 PILATUS3 6M 2016-02-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.03320 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.5 45.3 88.9 0.1 0.05 0.92 14.6 1.6 42427
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.54 46 0.52 0.33 0.71 1.4 1.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 3V47 2.5 45.272 2 41823 2086 89.77 0.2315 0.2295 0.2362 0.2703 0.2763
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 10.297 f_angle_d 1.105 f_chiral_restr 0.064 f_plane_restr 0.007 f_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9320 Nucleic Acid Atoms Solvent Atoms 121 Heterogen Atoms 74
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing