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Crystal structure of the TV8 hybrid of human TLR4 and hagfish VLRB.61
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Z62 PDB ENTRY 2Z62
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 277 0.2M Sodium Citrate, 0.1M Bis-Tris Propane, 27% PEG 1000, pH 6.50, VAPOR DIFFUSION, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.21 61.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.136 α = 90 b = 88.136 β = 90 c = 92.205 γ = 120
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 315 2007-04-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0 SPring-8 BL41XU
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 50 97 0.08 3.1 48960
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2Z62 2 20 50474 48960 2622 95.8 0.251 0.24961 0.2514 0.29809 0.2917 RANDOM 32.303
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] -0.49 -0.24 -0.49 0.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.341 r_dihedral_angle_3_deg 16.458 r_dihedral_angle_4_deg 13.751 r_scangle_it 5.344 r_dihedral_angle_1_deg 4.994 r_scbond_it 3.818 r_mcangle_it 2.161 r_mcbond_it 1.535 r_angle_refined_deg 1.38 r_nbtor_refined 0.319
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.341 r_dihedral_angle_3_deg 16.458 r_dihedral_angle_4_deg 13.751 r_scangle_it 5.344 r_dihedral_angle_1_deg 4.994 r_scbond_it 3.818 r_mcangle_it 2.161 r_mcbond_it 1.535 r_angle_refined_deg 1.38 r_nbtor_refined 0.319 r_symmetry_hbond_refined 0.233 r_nbd_refined 0.226 r_symmetry_vdw_refined 0.211 r_xyhbond_nbd_refined 0.156 r_chiral_restr 0.092 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4536 Nucleic Acid Atoms Solvent Atoms 292 Heterogen Atoms 66
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling