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Crystal structure of human TLR8 in complex with DS-877
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.4 293 10% (w/v) PEG 3350, 0.1M sodium citrate pH 4.4, 0.3M potassium formate, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.61 52.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 138.361 α = 90 b = 103.528 β = 106.74 c = 70.724 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 95 CCD ADSC QUANTUM 270 2013-06-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.0000 Photon Factory AR-NE3A
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 1.8 50 97 0.123 23.3 3.4 81803
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 1.81 27.19 80153 4237 96.51 0.17047 0.16846 0.1783 0.20782 0.2165 RANDOM 29.227
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] 0.01 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.676 r_dihedral_angle_4_deg 17.384 r_dihedral_angle_3_deg 14.677 r_long_range_B_refined 7.071 r_long_range_B_other 7.031 r_dihedral_angle_1_deg 6.829 r_scangle_other 5.717 r_scbond_it 3.788 r_scbond_other 3.787 r_mcangle_other 3.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.676 r_dihedral_angle_4_deg 17.384 r_dihedral_angle_3_deg 14.677 r_long_range_B_refined 7.071 r_long_range_B_other 7.031 r_dihedral_angle_1_deg 6.829 r_scangle_other 5.717 r_scbond_it 3.788 r_scbond_other 3.787 r_mcangle_other 3.12 r_mcangle_it 3.116 r_mcbond_it 2.413 r_mcbond_other 2.405 r_angle_refined_deg 2.048 r_angle_other_deg 0.966 r_chiral_restr 0.131 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 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 6013 Nucleic Acid Atoms Solvent Atoms 472 Heterogen Atoms 283
Software Software Software Name Purpose MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling