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Conversion of a Disulfide Bond into a Thioacetal Group during Echinomycin Biosynthesis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AMPLE generated Ensemble model from ROSETTA decoys
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.1 293 0.1M sodium cacodylate pH 6.1, 0.2M sodium acetate trihydrate, 30% (w/v) PEG 8000, 14% (v/v) ethylene glycol, 2.7% (w/v) sucrose, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.07 40.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.187 α = 90 b = 146.88 β = 102.63 c = 58.187 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS PILATUS 6M 2011-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.00 APS 17-ID
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 1.5 48.96 99.7 0.114 5.4 3.1 151355 22
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT AMPLE generated Ensemble model from ROSETTA decoys 1.5 45.42 143561 7689 99.68 0.15248 0.15042 0.19016 0.1983 RANDOM 18.066
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] 2.57 -5.44 -0.5 -2.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.645 r_sphericity_free 23.373 r_dihedral_angle_3_deg 12.151 r_dihedral_angle_4_deg 11.357 r_sphericity_bonded 7.748 r_dihedral_angle_1_deg 5.52 r_long_range_B_refined 2.454 r_long_range_B_other 2.452 r_scangle_other 1.777 r_mcangle_it 1.729
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.645 r_sphericity_free 23.373 r_dihedral_angle_3_deg 12.151 r_dihedral_angle_4_deg 11.357 r_sphericity_bonded 7.748 r_dihedral_angle_1_deg 5.52 r_long_range_B_refined 2.454 r_long_range_B_other 2.452 r_scangle_other 1.777 r_mcangle_it 1.729 r_mcangle_other 1.729 r_scbond_it 1.491 r_scbond_other 1.49 r_mcbond_it 1.362 r_mcbond_other 1.362 r_angle_refined_deg 1.17 r_rigid_bond_restr 0.807 r_angle_other_deg 0.709 r_chiral_restr 0.061 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7392 Nucleic Acid Atoms Solvent Atoms 320 Heterogen Atoms 245
Software Software Software Name Purpose MOSFLM data reduction AMPLE phasing REFMAC refinement Aimless data scaling SCALA data scaling