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Crystal structure of human TLR8 ectodomain bound to small molecule antagonist 14c
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3W3G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M magnesium formate, 20% (w/v) PEG 3,350, 10 mM praseodymium(III) acetate hydrate
Crystal Properties Matthews coefficient Solvent content 2.51 51.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 163.59 α = 90 b = 86.753 β = 119.8 c = 151.399 γ = 90
Symmetry Space Group C 1 2 1
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 PILATUS 6M 2016-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0 APS 17-ID
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 2.65 131.37 99.3 0.059 11.8 3.4 53326 75.41
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 2.65 2.79 99.9 0.483 2.3 3.3
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 3W3G 2.65 131.37 53257 2652 99.3 0.297 0.296 0.3245 0.306 0.3372 RANDOM 101.34
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] 1.5923 -5.1629 -20.1243 18.532
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.46 t_omega_torsion 1.5 t_angle_deg 0.97 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.46 t_omega_torsion 1.5 t_angle_deg 0.97 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11360 Nucleic Acid Atoms Solvent Atoms 40 Heterogen Atoms 605
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing BUSTER refinement PDB_EXTRACT data extraction