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The crystal structure of mouse TLR4/MD-2/lipid A complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Z64
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 0.1 M Tris, pH 8.0, 0.2 M lithium chloride, 14% PEG8000, 2.5% PEG400
Crystal Properties Matthews coefficient Solvent content 3.93 68.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.843 α = 90 b = 145.737 β = 100.67 c = 136.195 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 315r 2015-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97918 APS 19-ID
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 2.7 50 96.2 0.058 8.3 4 54848
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.75
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 5IJD 2.7 39.34 52860 1978 77.18 0.21727 0.21476 0.2172 0.28534 0.2836 RANDOM 43.652
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] -0.81 0.82 0.21 0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.606 r_dihedral_angle_4_deg 20.01 r_dihedral_angle_3_deg 18.137 r_long_range_B_refined 8.016 r_long_range_B_other 8.009 r_dihedral_angle_1_deg 7.782 r_scangle_other 4.808 r_mcangle_it 4.703 r_mcangle_other 4.703 r_mcbond_it 2.814
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.606 r_dihedral_angle_4_deg 20.01 r_dihedral_angle_3_deg 18.137 r_long_range_B_refined 8.016 r_long_range_B_other 8.009 r_dihedral_angle_1_deg 7.782 r_scangle_other 4.808 r_mcangle_it 4.703 r_mcangle_other 4.703 r_mcbond_it 2.814 r_mcbond_other 2.813 r_scbond_it 2.795 r_scbond_other 2.794 r_angle_other_deg 2.739 r_angle_refined_deg 1.8 r_chiral_restr 0.092 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_gen_planes_other 0.006 r_bond_other_d 0.001 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 11903 Nucleic Acid Atoms Solvent Atoms 232 Heterogen Atoms 242
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing