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Crystal structure of the TV3 hybrid of human TLR4 and hagfish VLRB.61
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZIW PDB ENTRY 1ZIW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.5 296 0.2M NaCl, 0.1M Bis-Tris Propane, 33% PEG 1000, pH 5.50, VAPOR DIFFUSION, temperature 296K
Crystal Properties Matthews coefficient Solvent content 2.23 44.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.945 α = 90 b = 54.214 β = 90 c = 116.637 γ = 90
Symmetry Space Group P 21 21 21
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 ADSC QUANTUM 210 2006-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 4A 1.0 PAL/PLS 4A
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 1.7 50 99.1 0.06 6.6 29573
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1ZIW 1.7 20 29841 29573 1588 99.1 0.19 0.19 0.1924 0.208 RANDOM 27.115
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] -0.21 -0.5 0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.843 r_dihedral_angle_4_deg 19.356 r_dihedral_angle_3_deg 13.485 r_dihedral_angle_1_deg 5.275 r_angle_refined_deg 1.188 r_nbtor_refined 0.317 r_symmetry_hbond_refined 0.304 r_symmetry_vdw_refined 0.235 r_nbd_refined 0.197 r_xyhbond_nbd_refined 0.108
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.843 r_dihedral_angle_4_deg 19.356 r_dihedral_angle_3_deg 13.485 r_dihedral_angle_1_deg 5.275 r_angle_refined_deg 1.188 r_nbtor_refined 0.317 r_symmetry_hbond_refined 0.304 r_symmetry_vdw_refined 0.235 r_nbd_refined 0.197 r_xyhbond_nbd_refined 0.108 r_chiral_restr 0.078 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it 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 2189 Nucleic Acid Atoms Solvent Atoms 242 Heterogen Atoms 115
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling