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High resolution crystal structure of LuxS - Quorum sensor molecular complex from Salmonella typhi at 1.58 Angstroms
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JOE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 Sodium formate, Bis-trispropane, PEG3350
Crystal Properties Matthews coefficient Solvent content 2.05 39.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.345 α = 90 b = 66.427 β = 106.17 c = 54.31 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 MARMOSAIC 225 mm CCD 2014-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97625 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.58 50 98.4 2.31 7.9 59402
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 1.58 1.61 98.5 2.31 2.31
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 1JOE 1.58 30.71 42158 2234 98.43 0.16228 0.16043 0.1731 0.19645 0.2026 RANDOM 22.286
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] -1.91 -0.15 1.71 0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.561 r_dihedral_angle_4_deg 20.144 r_dihedral_angle_3_deg 11.815 r_long_range_B_refined 6.631 r_long_range_B_other 6.578 r_dihedral_angle_1_deg 6.484 r_scangle_other 4.966 r_scbond_it 3.49 r_scbond_other 3.487 r_mcangle_it 3.189
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.561 r_dihedral_angle_4_deg 20.144 r_dihedral_angle_3_deg 11.815 r_long_range_B_refined 6.631 r_long_range_B_other 6.578 r_dihedral_angle_1_deg 6.484 r_scangle_other 4.966 r_scbond_it 3.49 r_scbond_other 3.487 r_mcangle_it 3.189 r_mcangle_other 3.189 r_mcbond_it 2.364 r_mcbond_other 2.35 r_angle_refined_deg 2.181 r_angle_other_deg 1.393 r_chiral_restr 0.16 r_bond_refined_d 0.025 r_gen_planes_refined 0.013 r_bond_other_d 0.01 r_gen_planes_other 0.008 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 2622 Nucleic Acid Atoms Solvent Atoms 227 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement HKL-2000 data processing BALBES phasing