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Crystal structure of an omega-transaminase mutant I77L/Q97E/H210N/N245D from Aspergillus terreus in complex with PLP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4CE5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291.15 100 mM citrate buffer (pH 7.5)
200 mM ammonium acetate
4% (w/v) PEG-MME 8000
1 mM pyridoxal phosphate
Crystal Properties Matthews coefficient Solvent content 2.98 58.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.42 α = 90 b = 135.79 β = 90 c = 116.93 γ = 90
Symmetry Space Group C 2 2 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 2023-11-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97861 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.09 41.881 97.5 0.104 0.114 0.034 16.4 5.5 49080
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.09 9.35 82.9 0.875 0.987 0.441 1.6 4.7
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 THROUGHOUT 2.09 41.881 1.37 49044 2416 97.37 0.1733 0.1711 0.1724 0.2164 0.2177
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 12.19 f_angle_d 0.818 f_chiral_restr 0.056 f_bond_d 0.008 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4986 Nucleic Acid Atoms Solvent Atoms 497 Heterogen Atoms 32
Software Software Software Name Purpose PHENIX refinement HKL-3000 data scaling HKL-3000 data reduction AMPLE phasing PDB_EXTRACT data extraction