☰ Navigation Tabs
Crystal structure of the VT3 hybrid of human TLR4 and hagfish VLRB.61
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 5.5 277 0.2M Lithium Sulfate, 0.1M Sodium Acetate, 24% PEG 4000, pH 5.50, temperature 277K, VAPOR DIFFUSION
Crystal Properties Matthews coefficient Solvent content 3.02 59.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.787 α = 89.86 b = 67.971 β = 89.96 c = 122.779 γ = 90.01
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 2007-03-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 1.0 ESRF ID14-3
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 1.9 50 93.7 0.09 2.6 112862
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 2Z63 1.9 20 120450 112862 5929 93.7 0.20966 0.20917 0.2112 0.21908 0.2205 RANDOM 13.368
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] -0.19 -0.1 -0.1 0.29 0.03 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.911 r_dihedral_angle_4_deg 15.211 r_dihedral_angle_3_deg 12.099 r_dihedral_angle_1_deg 4.932 r_scangle_it 4.715 r_scbond_it 3.367 r_mcangle_it 1.877 r_mcbond_it 1.416 r_angle_refined_deg 1.098 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.911 r_dihedral_angle_4_deg 15.211 r_dihedral_angle_3_deg 12.099 r_dihedral_angle_1_deg 4.932 r_scangle_it 4.715 r_scbond_it 3.367 r_mcangle_it 1.877 r_mcbond_it 1.416 r_angle_refined_deg 1.098 r_nbtor_refined 0.314 r_symmetry_vdw_refined 0.291 r_nbd_refined 0.217 r_symmetry_hbond_refined 0.114 r_xyhbond_nbd_refined 0.104 r_chiral_restr 0.065 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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9620 Nucleic Acid Atoms Solvent Atoms 472 Heterogen Atoms 596
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling