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The structure of SdnG covalently binding with the cope rearrangement product
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8YHG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 289.15 0.1M MOPSO/bis-tris pH 6.5, 5%(w/v) PEG 20K, 25% (w/v) 1,1,1tris(hydroxymethyl)propane, 1%(w/v) NDSB 195, 0.5mM of each Lanthanide: 5mM erbium(III) chloride hexahydrate, 5mM terbium(III) chloride hexahydrate, 5mM ytterbium(III) chloride hexahydrate, 5mM yttrium(III) chloride hexahydrate
Crystal Properties Matthews coefficient Solvent content 2.11 41.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.83 α = 90 b = 59.31 β = 90 c = 107.74 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 PILATUS3 6M 2022-03-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97915 SSRF BL18U1
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 1.72 39.88 100 0.082 18.9 12.8 31340 25.11
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 1.72 1.75 1.35 0.803
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 1.72 39.88 1.35 31277 1557 99.95 0.1914 0.1902 0.1916 0.2158 0.2158 34.98
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 15.4977 f_angle_d 0.7297 f_chiral_restr 0.0556 f_plane_restr 0.0053 f_bond_d 0.0033
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1910 Nucleic Acid Atoms Solvent Atoms 208 Heterogen Atoms 230
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing