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The TIR domain of human Toll-Like Receptor 10 (TLR10)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FYV PDB ENTRY 1FYV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.2 M NASCN, 11% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.89 57.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.2 α = 90 b = 43.3 β = 101 c = 71.3 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 100 CCD MARRESEARCH 2006-08-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.2 23 97.6 0.06 13.8 3.8 19993
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.3 92 0.4 3.5 3.7
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 PDB ENTRY 1FYV 2.2 23.43 18992 1000 97.8 0.216 0.214 0.2189 0.266 0.2669 RANDOM 28.04
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] -2.02 -0.93 1.53 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.406 r_dihedral_angle_4_deg 20.217 r_dihedral_angle_3_deg 15.871 r_dihedral_angle_1_deg 6.933 r_scangle_it 2.532 r_scbond_it 2.187 r_mcangle_it 1.714 r_angle_refined_deg 1.524 r_mcbond_it 1.356 r_angle_other_deg 0.954
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.406 r_dihedral_angle_4_deg 20.217 r_dihedral_angle_3_deg 15.871 r_dihedral_angle_1_deg 6.933 r_scangle_it 2.532 r_scbond_it 2.187 r_mcangle_it 1.714 r_angle_refined_deg 1.524 r_mcbond_it 1.356 r_angle_other_deg 0.954 r_nbd_refined 0.226 r_nbtor_refined 0.198 r_xyhbond_nbd_refined 0.192 r_symmetry_vdw_other 0.19 r_nbd_other 0.188 r_symmetry_hbond_refined 0.171 r_symmetry_vdw_refined 0.144 r_chiral_restr 0.097 r_nbtor_other 0.086 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2345 Nucleic Acid Atoms Solvent Atoms 117 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing