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Crystal structure of human TLR8 in complex with XG-1-236
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.2 293 12%(w/v) PEG3350, 0.1M sodium citrate, 0.3M potassium formate, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.4 48.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.51 α = 90 b = 149.22 β = 103.5 c = 85.83 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 PIXEL DECTRIS PILATUS 6M 2013-04-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0000 SPring-8 BL41XU
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 2.1 83.46 88.8 0.11 6 2.8 96489
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 2.1 83.46 85502 4509 88.48 0.21631 0.21336 0.2183 0.27137 0.2735 RANDOM 37.087
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] 0.02 0.02 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.925 r_dihedral_angle_4_deg 22.224 r_dihedral_angle_3_deg 17.415 r_dihedral_angle_1_deg 7.274 r_long_range_B_refined 6.292 r_long_range_B_other 6.289 r_scangle_other 4.244 r_mcangle_it 3.714 r_mcangle_other 3.714 r_scbond_it 2.687
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.925 r_dihedral_angle_4_deg 22.224 r_dihedral_angle_3_deg 17.415 r_dihedral_angle_1_deg 7.274 r_long_range_B_refined 6.292 r_long_range_B_other 6.289 r_scangle_other 4.244 r_mcangle_it 3.714 r_mcangle_other 3.714 r_scbond_it 2.687 r_scbond_other 2.686 r_mcbond_it 2.443 r_mcbond_other 2.443 r_angle_refined_deg 1.684 r_angle_other_deg 0.87 r_chiral_restr 0.088 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.002 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 11984 Nucleic Acid Atoms Solvent Atoms 176 Heterogen Atoms 273
Software Software Software Name Purpose MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling