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Human TLR8 ectodomain with small molecule agonist 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3W3J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 0.2 M magnesium formate, 20% (w/v) PEG 3,350, 0.1 M TCEP
Crystal Properties Matthews coefficient Solvent content 2.34 47.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.58 α = 116.05 b = 82.41 β = 97.71 c = 83.44 γ = 98.68
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 EIGER2 X 9M 2020-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.66 73.03 81.1 0.999 13.9 1.8 202912
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.66 1.83 0.615 1.7
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 1.66 73.03 121156 6152 61.3 0.202 0.201 0.204 0.223 0.2286 RANDOM 37.15
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] -0.6744 -0.602 0.1985 1.9343 0.1217 -1.2599
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 14.92 t_omega_torsion 3.47 t_angle_deg 1 t_bond_d 0.008 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 14.92 t_omega_torsion 3.47 t_angle_deg 1 t_bond_d 0.008 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion 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 12023 Nucleic Acid Atoms Solvent Atoms 1079 Heterogen Atoms 615
Software Software Software Name Purpose XDS data reduction XDS data scaling PHASER phasing BUSTER refinement