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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 54.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.782 α = 90 b = 66.782 β = 90 c = 116.336 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 2021-03-03 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 2.04 30 100 0.07 32.84 11.6 19749 33.5243086976
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.04 2.11 0.738
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 2.04001020299 28.9588223376 1.36651513816 19711 973 99.9442247237 0.201582819044 0.199336969955 0.1997 0.244796606859 0.246 34.6291999048
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 13.1389898211 f_angle_d 0.968056282015 f_chiral_restr 0.061482104077 f_bond_d 0.00749877669757 f_plane_restr 0.00651007393658
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1756 Nucleic Acid Atoms Solvent Atoms 103 Heterogen Atoms 35
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing