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Crystal structure of the human TLR4 TV3 hybrid-MD-2-Eritoran complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Z62 PDB ENTRY 2Z62, 2Z64 experimental model PDB 2Z64 PDB ENTRY 2Z62, 2Z64
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 4.5 296 0.2M Ammonium Sulfate, 0.1M Sodium Acetate, 20% PEG 4000, 5% Ethanol, pH 4.5, VAPOR DIFFUSION, temperature 296K
Crystal Properties Matthews coefficient Solvent content 3.09 60.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.192 α = 90 b = 80.987 β = 93.01 c = 107.762 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 ADSC QUANTUM 315 mirrors 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 2.7 50 90.4 0.089 3 30860 27898
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 2Z62, 2Z64 2.7 20 27898 1462 92.35 0.2403 0.23763 0.2308 0.28874 0.2817 RANDOM 50.542
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] 2.91 -1.93 -2.26 -0.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.442 r_dihedral_angle_3_deg 18.508 r_dihedral_angle_4_deg 17.737 r_scangle_it 9.905 r_scbond_it 6.769 r_dihedral_angle_1_deg 6.584 r_mcangle_it 4.228 r_mcbond_it 2.658 r_angle_refined_deg 1.393 r_nbtor_refined 0.319
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.442 r_dihedral_angle_3_deg 18.508 r_dihedral_angle_4_deg 17.737 r_scangle_it 9.905 r_scbond_it 6.769 r_dihedral_angle_1_deg 6.584 r_mcangle_it 4.228 r_mcbond_it 2.658 r_angle_refined_deg 1.393 r_nbtor_refined 0.319 r_symmetry_vdw_refined 0.26 r_nbd_refined 0.232 r_xyhbond_nbd_refined 0.172 r_symmetry_hbond_refined 0.16 r_chiral_restr 0.087 r_bond_refined_d 0.01 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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6646 Nucleic Acid Atoms Solvent Atoms 163 Heterogen Atoms 287
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling