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Crystal structure of mouse TLR4 and mouse MD-2 complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Z63 PDB ENTRY 2Z63
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 296 0.1M Na-Cacodylate, 23% PEG 8000, pH 6.5, VAPOR DIFFUSION, temperature 296K
Crystal Properties Matthews coefficient Solvent content 3.21 61.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.158 α = 90 b = 101.882 β = 90 c = 126.364 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 mirrors 2007-04-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 1.0 ALS 5.0.1
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 2.8 50 90.1 0.095 4.6 23932
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 2Z63 2.84 20 22180 1183 90.1 0.24449 0.24206 0.2288 0.29043 0.2717 RANDOM 30.87
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] 0.87 -5.87 5.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.946 r_dihedral_angle_4_deg 19.556 r_dihedral_angle_3_deg 18.404 r_scangle_it 6.952 r_dihedral_angle_1_deg 5.814 r_scbond_it 4.426 r_mcangle_it 2.793 r_mcbond_it 1.602 r_angle_refined_deg 1.421 r_nbtor_refined 0.325
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.946 r_dihedral_angle_4_deg 19.556 r_dihedral_angle_3_deg 18.404 r_scangle_it 6.952 r_dihedral_angle_1_deg 5.814 r_scbond_it 4.426 r_mcangle_it 2.793 r_mcbond_it 1.602 r_angle_refined_deg 1.421 r_nbtor_refined 0.325 r_symmetry_hbond_refined 0.286 r_nbd_refined 0.247 r_symmetry_vdw_refined 0.236 r_xyhbond_nbd_refined 0.159 r_chiral_restr 0.087 r_bond_refined_d 0.01 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 5867 Nucleic Acid Atoms Solvent Atoms 154 Heterogen Atoms 281
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling