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Crystal structure of horse TLR9 in complex with two DNAs (CpG DNA and GCGCAC DNA)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WPC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 4-6%(w/v) PEG 4000, 4-6%(v/v) 2-propanol, 0.2M NaCl, 0.1M citrate-NaoH pH 5.6
Crystal Properties Matthews coefficient Solvent content 2.49 50.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.849 α = 90 b = 126.502 β = 98.49 c = 140.716 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 100 PIXEL DECTRIS PILATUS3 6M 2015-06-28 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) 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 2.7 47.14 98.9 12 3.5 50239
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 3WPC 2.7 47.14 47705 2533 98.81 0.20739 0.20533 0.2095 0.24552 0.2456 RANDOM 62.364
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] 2.38 1.01 -2.96 0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.708 r_dihedral_angle_4_deg 17.71 r_dihedral_angle_3_deg 14.546 r_dihedral_angle_1_deg 6.45 r_long_range_B_refined 5.093 r_long_range_B_other 5.092 r_scangle_other 3.224 r_mcangle_other 3.167 r_mcangle_it 3.166 r_scbond_it 1.884
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.708 r_dihedral_angle_4_deg 17.71 r_dihedral_angle_3_deg 14.546 r_dihedral_angle_1_deg 6.45 r_long_range_B_refined 5.093 r_long_range_B_other 5.092 r_scangle_other 3.224 r_mcangle_other 3.167 r_mcangle_it 3.166 r_scbond_it 1.884 r_scbond_other 1.884 r_mcbond_it 1.867 r_mcbond_other 1.864 r_angle_refined_deg 1.446 r_angle_other_deg 1.003 r_chiral_restr 0.071 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 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 11786 Nucleic Acid Atoms 644 Solvent Atoms 70 Heterogen Atoms 266
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing