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Crystal structure of human TLR8 in complex with Hybrid-2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.9 293 10%(w/v) PEG3350, 0.1M sodium citrate pH 4.9, 0.3M potassium formate, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.52 51.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.143 α = 90 b = 122.211 β = 91.13 c = 107.778 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 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 2.1 50 87.1 0.1 17 2.7 89651
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 26.09 80433 4733 86.7 0.20375 0.20084 0.2077 0.25932 0.2616 RANDOM 38.476
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 40.678 r_dihedral_angle_3_deg 17.816 r_dihedral_angle_4_deg 16.723 r_dihedral_angle_1_deg 7.876 r_long_range_B_refined 7.451 r_long_range_B_other 7.447 r_scangle_other 5.333 r_mcangle_it 4.322 r_mcangle_other 4.321 r_scbond_it 3.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.678 r_dihedral_angle_3_deg 17.816 r_dihedral_angle_4_deg 16.723 r_dihedral_angle_1_deg 7.876 r_long_range_B_refined 7.451 r_long_range_B_other 7.447 r_scangle_other 5.333 r_mcangle_it 4.322 r_mcangle_other 4.321 r_scbond_it 3.39 r_scbond_other 3.389 r_mcbond_it 2.86 r_mcbond_other 2.86 r_angle_refined_deg 1.65 r_angle_other_deg 0.786 r_chiral_restr 0.091 r_bond_refined_d 0.012 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 11973 Nucleic Acid Atoms Solvent Atoms 402 Heterogen Atoms 441
Software Software Software Name Purpose MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling