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Crystal structure of human TLR8 in complex with N1-4-aminomethylbenzyl (IMDQ)
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 2.7 54.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.66 α = 90 b = 106.67 β = 106.24 c = 72.16 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 2013-11-09 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 2.05 82.526 99.8 9.6 3.5 61824
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 2.05 69.28 58440 3116 99.57 0.21733 0.2146 0.26901 0.2673 RANDOM 38.436
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
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.392 r_dihedral_angle_3_deg 17.203 r_dihedral_angle_4_deg 13.968 r_long_range_B_refined 7.797 r_long_range_B_other 7.797 r_dihedral_angle_1_deg 7.475 r_scangle_other 5.891 r_mcangle_it 4.417 r_mcangle_other 4.417 r_scbond_it 3.898
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.392 r_dihedral_angle_3_deg 17.203 r_dihedral_angle_4_deg 13.968 r_long_range_B_refined 7.797 r_long_range_B_other 7.797 r_dihedral_angle_1_deg 7.475 r_scangle_other 5.891 r_mcangle_it 4.417 r_mcangle_other 4.417 r_scbond_it 3.898 r_scbond_other 3.895 r_mcbond_it 3.154 r_mcbond_other 3.145 r_angle_refined_deg 1.608 r_angle_other_deg 0.778 r_chiral_restr 0.095 r_bond_refined_d 0.011 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 6037 Nucleic Acid Atoms Solvent Atoms 308 Heterogen Atoms 253
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing