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Directed Evolution of Transaminases By Ancestral Reconstruction. Using Old Proteins for New Chemistries
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GJU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.8 293 150 nL plus 150 nL drops of protein at 5 mg/mL and reservoir which consisted of 1.6 M ammonium sulfate, 1% dioxane, 50 mM MES pH 6.8
Crystal Properties Matthews coefficient Solvent content 2.12 41.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.346 α = 90 b = 66.346 β = 90 c = 343.314 γ = 120
Symmetry Space Group P 65 2 2
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 ADSC QUANTUM 315r 2013-05-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.99 47.8 99.9 0.136 0.998 17.6 20.7 32214
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.99 2.1 99.3 0.72 0.91 4.9 20.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 3gju 1.99 47.8 30450 1625 99.89 0.19778 0.19569 0.2039 0.23695 0.2422 RANDOM 23.889
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] -0.28 -0.14 -0.28 0.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.578 r_dihedral_angle_4_deg 17.272 r_dihedral_angle_3_deg 13.53 r_dihedral_angle_1_deg 6.702 r_long_range_B_refined 3.661 r_long_range_B_other 3.661 r_scangle_other 2.016 r_mcangle_it 1.641 r_mcangle_other 1.641 r_angle_refined_deg 1.389
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.578 r_dihedral_angle_4_deg 17.272 r_dihedral_angle_3_deg 13.53 r_dihedral_angle_1_deg 6.702 r_long_range_B_refined 3.661 r_long_range_B_other 3.661 r_scangle_other 2.016 r_mcangle_it 1.641 r_mcangle_other 1.641 r_angle_refined_deg 1.389 r_scbond_it 1.243 r_scbond_other 1.243 r_mcbond_it 1.057 r_mcbond_other 1.057 r_angle_other_deg 0.955 r_chiral_restr 0.079 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 3447 Nucleic Acid Atoms Solvent Atoms 182 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing