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Complex structure of N-acetyltransferase SbzI and carrier protein SbzG in the biosynthesis of altemicidin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M MES, pH 6.5, 0.2 M KSCN, 15% PEG 8000, 3% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 3.83 67.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.15 α = 90 b = 95.68 β = 90 c = 130.79 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2023-06-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0 SPring-8 BL41XU
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 2.6 47.84 99.9 0.12 23.3 18 30470 61.43
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.72 99.9 1.168 0.947 4.5 18.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE AlphaFold 2.6 47.84 1.37 30416 2000 99.85 0.1984 0.1959 0.2343 0.244 82.59
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 13.4293 f_angle_d 0.7068 f_chiral_restr 0.0408 f_plane_restr 0.0071 f_bond_d 0.0046
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3768 Nucleic Acid Atoms Solvent Atoms 47 Heterogen Atoms 69
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing