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Structural and mechanistic studies of a novel non-heme iron epimerase/lyase and its utilization in chemoselective synthesis.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6J4C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 1.2 M Sodium phosphate monobasic monohydrate, Potassium phosphate dibasic, pH 7.8
Crystal Properties Matthews coefficient Solvent content 2.71 54.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.822 α = 90 b = 66.822 β = 90 c = 116.388 γ = 120
Symmetry Space Group P 32 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 MX300HE 2020-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 1 NSRRC BL15A1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.11 30 96.6 0.046 25.7 7.5 17329 31.4590347307
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.11 2.19 0.524
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 NONE 6J4C 2.1104343131 23.1942902442 1.3677339183 17326 866 96.8798926415 0.189370246055 0.187658305014 0.1885 0.221082238527 0.2222 32.8330893076
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 13.0606984527 f_angle_d 1.36369365463 f_chiral_restr 0.0802972000487 f_bond_d 0.009687337715 f_plane_restr 0.00676135286013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1730 Nucleic Acid Atoms Solvent Atoms 69 Heterogen Atoms 28
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing