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PLP and 1-Boc-2-methyl-piperidin-5-one complex structure of an (R)-selective omega-transaminase from Ancylobacter lacus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.3 293.15 0.05M Magnesium chloride hexahydrate, 0.1M MES, 5%w/v PEG4000, 10% 2-Propanol
Crystal Properties Matthews coefficient Solvent content 2.54 46.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.83 α = 74.64 b = 72.45 β = 85.69 c = 84.32 γ = 69.92
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 2024-10-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97853 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.93 23.39 96.3 0.982 7.2 3.5 102179
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.93 1.96 0.535
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 1.93 23.39 1.96 102160 2000 96.33 0.1883 0.1876 0.1876 0.2242 0.2238
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 11.989 f_angle_d 0.975 f_chiral_restr 0.059 f_bond_d 0.007 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9994 Nucleic Acid Atoms Solvent Atoms 1190 Heterogen Atoms 60
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHENIX phasing