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Crystal structure of a nonribosomal peptide synthetase heterocyclization domain.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JN3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 BmdB-Cy2 was crystallized by mixing with 0.88% Tween 20, 1.62 M ammonium sulfate, 0.1 M HEPES pH 7.5, 2.67% PEG 400, and 3% 6-aminohexanoic acid, and equilibrated 0.88% Tween 20, 1.62 M ammonium sulfate, 0.1 M HEPES pH 7.5, 2.67% PEG 400, and 3% 6-aminohexanoic acid. Crystals were transferred into a solution of mother liquor plus 20% (v/v) ethylene glycol, and flash-cooled in liquid nitrogen.
Crystal Properties Matthews coefficient Solvent content 2.89 57.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.693 α = 90 b = 124.937 β = 95.66 c = 68.925 γ = 90
Symmetry Space Group C 1 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 RAYONIX MX-300 2015-10-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 CLSI 08ID-1
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 2.3 39.9 99.8 15.1 3.1 52064
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4JN3 2.297 39.894 1.36 52042 2623 99.28 0.2024 0.2006 0.2029 0.2371 0.238
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 17.943 f_angle_d 0.773 f_chiral_restr 0.05 f_plane_restr 0.005 f_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7003 Nucleic Acid Atoms Solvent Atoms 217 Heterogen Atoms 10
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing