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Crystal structure of horse TLR9 in complex with two DNAs (CpG DNA and TCGCAC 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 2%(w/v) PEG10000, 20mM Mg-acetate, 20mM Mes-NaOH pH6.5
Crystal Properties Matthews coefficient Solvent content 2.52 51.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.493 α = 90 b = 125.199 β = 94.78 c = 139.294 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 1.81 49.4 98.9 8.6 3.5 167790
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 1.81 49.4 159206 8576 98.8 0.17941 0.17798 0.1867 0.20641 0.216 RANDOM 26.344
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] 0.19 0.62 -0.86 0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.026 r_dihedral_angle_4_deg 17.403 r_dihedral_angle_3_deg 12.675 r_long_range_B_refined 6.987 r_long_range_B_other 6.635 r_dihedral_angle_1_deg 6.587 r_scangle_other 2.789 r_scbond_it 1.69 r_scbond_other 1.69 r_angle_refined_deg 1.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.026 r_dihedral_angle_4_deg 17.403 r_dihedral_angle_3_deg 12.675 r_long_range_B_refined 6.987 r_long_range_B_other 6.635 r_dihedral_angle_1_deg 6.587 r_scangle_other 2.789 r_scbond_it 1.69 r_scbond_other 1.69 r_angle_refined_deg 1.68 r_mcangle_it 1.664 r_mcangle_other 1.664 r_angle_other_deg 1.068 r_mcbond_it 1.012 r_mcbond_other 1.011 r_chiral_restr 0.096 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 640 Solvent Atoms 2078 Heterogen Atoms 268
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing