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Crystal structure of human TLR8 in complex with N1-3-aminomethylbenzyl (meta-amine)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 PEG3350, potassium formate, sodium citrate
Crystal Properties Matthews coefficient Solvent content 2.69 54.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.9 α = 90 b = 107.05 β = 106.35 c = 72.089 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) 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 50 98.9 26.4 3.1 55948
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION THROUGHOUT 2.1 27.5 53673 2872 98.65 0.20364 0.20062 0.25905 0.2619 RANDOM 50.112
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] 0.04 -0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.675 r_dihedral_angle_3_deg 16.586 r_dihedral_angle_4_deg 13.816 r_long_range_B_other 8.602 r_long_range_B_refined 8.596 r_dihedral_angle_1_deg 7.212 r_scangle_other 6.824 r_mcangle_it 5.344 r_mcangle_other 5.344 r_scbond_it 4.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.675 r_dihedral_angle_3_deg 16.586 r_dihedral_angle_4_deg 13.816 r_long_range_B_other 8.602 r_long_range_B_refined 8.596 r_dihedral_angle_1_deg 7.212 r_scangle_other 6.824 r_mcangle_it 5.344 r_mcangle_other 5.344 r_scbond_it 4.61 r_scbond_other 4.61 r_mcbond_it 3.991 r_mcbond_other 3.989 r_angle_refined_deg 1.893 r_angle_other_deg 0.89 r_chiral_restr 0.104 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.001 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 6018 Nucleic Acid Atoms Solvent Atoms 190 Heterogen Atoms 186
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing