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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 54.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.791 α = 90 b = 66.791 β = 90 c = 116.595 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 2020-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 05A 1 NSRRC TPS 05A
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 2.087 30 100 0.06 26.74 11.7 18506 30.9923688362
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 2.09 2.16 0.593
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 2.08757062717 28.9777017687 1.35884687413 18469 923 99.9675236806 0.192976267174 0.190932481955 0.1915 0.232961939324 0.2343 30.0567027247
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 14.6043050231 f_angle_d 1.07372197425 f_chiral_restr 0.0837026347286 f_bond_d 0.00806240125198 f_plane_restr 0.00680079839044
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1709 Nucleic Acid Atoms Solvent Atoms 105 Heterogen Atoms 32
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing