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Crystal structure of a complex between Bacillus subtilis flagellin and zebrafish Toll-like receptor 5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3V47
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.4 291 PEG 300, sodium acetate, pH 4.4
Crystal Properties Matthews coefficient Solvent content 2.47 50.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.146 α = 90 b = 54.281 β = 98.62 c = 165.98 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 2013-06-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 0.9796 PAL/PLS 5C (4A)
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 2.1 30 98.1 0.091 16.8 3.4 80115
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 3V47 2.1 30 75311 3987 97.95 0.19691 0.19477 0.1998 0.23627 0.2382 RANDOM 33.3
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] 0.3 1.11 0.55 -0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.542 r_dihedral_angle_4_deg 22.421 r_dihedral_angle_3_deg 14.559 r_dihedral_angle_1_deg 5.946 r_scangle_it 4.461 r_angle_other_deg 4.28 r_scbond_it 2.64 r_angle_refined_deg 1.507 r_mcangle_it 1.371 r_mcbond_it 0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.542 r_dihedral_angle_4_deg 22.421 r_dihedral_angle_3_deg 14.559 r_dihedral_angle_1_deg 5.946 r_scangle_it 4.461 r_angle_other_deg 4.28 r_scbond_it 2.64 r_angle_refined_deg 1.507 r_mcangle_it 1.371 r_mcbond_it 0.71 r_chiral_restr 0.091 r_bond_refined_d 0.016 r_gen_planes_other 0.008 r_gen_planes_refined 0.006 r_bond_other_d 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9429 Nucleic Acid Atoms Solvent Atoms 465 Heterogen Atoms 166
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing