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Crystal structure of an omega-transaminase mutant from Aspergillus terreus with 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 5.6 291.15 100 mM citrate buffer (pH 5.6)
200 mM ammonium acetate
30% (w/v) PEG-MME 4000
0.1 mM pyridoxal phosphate
Crystal Properties Matthews coefficient Solvent content 3.81 67.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.436 α = 90 b = 113.983 β = 91.56 c = 101.424 γ = 90
Symmetry Space Group I 1 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 PIXEL DECTRIS PILATUS3 6M 2023-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.9785 SSRF BL18U1
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 2.3 47 97.6 0.126 0.162 0.1 6.1 3.9 46471 34.89
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 2.3 2.38 98.4 0.556 0.716 0.446 3.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.3 47 43949 2519 97.46 0.22333 0.2211 0.2356 0.26246 0.2692 RANDOM 36.916
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] 1.45 -5.73 -2.61 1.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.035 r_dihedral_angle_2_deg 8.599 r_dihedral_angle_1_deg 7.272 r_long_range_B_refined 5.863 r_long_range_B_other 5.855 r_scangle_other 4.405 r_mcangle_it 3.899 r_mcangle_other 3.899 r_scbond_it 2.907 r_scbond_other 2.906
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.035 r_dihedral_angle_2_deg 8.599 r_dihedral_angle_1_deg 7.272 r_long_range_B_refined 5.863 r_long_range_B_other 5.855 r_scangle_other 4.405 r_mcangle_it 3.899 r_mcangle_other 3.899 r_scbond_it 2.907 r_scbond_other 2.906 r_mcbond_it 2.63 r_mcbond_other 2.625 r_angle_refined_deg 1.452 r_angle_other_deg 0.492 r_chiral_restr 0.064 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5028 Nucleic Acid Atoms Solvent Atoms 159 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling HKL-3000 data reduction AMPLE phasing PDB_EXTRACT data extraction