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Crystal structure of the ferric enterobactin transporter (XusB) from Bacteroides thetaiotaomicron
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold Q8A622
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 2 M ammonium sulfate, 0.1 M sodium cacodylate (pH 6.5), and 0.2 M sodium chloride, and 0.1 M Sodium citrate tribasic dihydrate
Crystal Properties Matthews coefficient Solvent content 4.76 74.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 174.193 α = 90 b = 174.193 β = 90 c = 294.28 γ = 120
Symmetry Space Group P 31 2 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 300 mm CCD 2022-07-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.9786 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.55 29.9 99.8 0.997 15.38 3.8 167888 44.96
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.55 2.59 0.841 2.02
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE 2.55 29.9 1.33 167888 8535 99.8 0.225 0.224 0.2321 0.247 0.2498 RANDOM
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 11.698 f_angle_d 0.488 f_chiral_restr 0.044 f_plane_restr 0.003 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18781 Nucleic Acid Atoms Solvent Atoms 281 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction Coot model building HKL-2000 data scaling PHENIX phasing