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Structure of FbsH, an NRPS adenylation domain in the fimsbactin biosynthetic pathway bound to 2,3-dihydroxybenzoic acid.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold N-term Subdomain, 1-441.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 287.15 0.1M HEPES pH 7.5, 12% PEG 3350, 0.5 mM DHB, 0.5 mM AMP
Crystal Properties Matthews coefficient Solvent content 2.31 46.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.41 α = 85.04 b = 74.478 β = 69.89 c = 75.493 γ = 70.29
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93.15 PIXEL DECTRIS PILATUS3 6M 2023-03-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.03373 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.3 35.62 98.25 0.128 0.1523 0.08125 0.99 10.32 3.5 47445 42
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.382 97.14 0.9187 1 0.5656 0.44 1.42
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.3 35.62 1.96 47424 2239 96.16 0.1943 0.1926 0.1933 0.2352 0.2377 37.04
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 8.7802 f_angle_d 0.6309 f_chiral_restr 0.0472 f_plane_restr 0.0049 f_bond_d 0.0042
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7747 Nucleic Acid Atoms Solvent Atoms 183 Heterogen Atoms 30
Software Software Software Name Purpose PHENIX refinement xia2 data reduction xia2 data scaling PHASER phasing