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Structure of 3-amino-3-carboxyltransferase in complex with SAH and nocardicin G in the biosynthesis of nocardicins
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 298 20% (w/v) PEG 3350, 200 mM Ammonium nitrate pH 6.3
Crystal Properties Matthews coefficient Solvent content 1.91 35.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.221 α = 90 b = 76.582 β = 90 c = 146.758 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 4M 2024-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.02 Photon Factory BL-1A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.13 48.92 100 0.14 0.997 11.1 7.5 31289 26.29
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 2.13 2.19 100 0.887 0.768 2.2 7.8
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE AlphaFold 2.13 45.81 29550 1898 94.6 0.1853 0.1822 0.1799 0.2295 0.2247 30.18
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 9.1106 f_angle_d 0.9518 f_chiral_restr 0.0515 f_plane_restr 0.0082 f_bond_d 0.0072
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4324 Nucleic Acid Atoms Solvent Atoms 197 Heterogen Atoms 101
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing