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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 5KQT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 150 plus 150 nL drops with protein at 10 mg/mL and reservoir conditions of 16% PEG 3350, 215 mM ammonium formate. Microseeds were used to produce full size crystals.
Crystal Properties Matthews coefficient Solvent content 2.01 38.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.088 α = 90 b = 123.24 β = 117.61 c = 63.251 γ = 90
Symmetry Space Group P 1 21 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 ADSC QUANTUM 315r 2014-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.95370 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 48.8 98.5 0.075 0.995 13 3.7 55970
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 2.04 98.1 0.32 0.859 3.4 3.6
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5kqt 1.99 48.8 53036 2651 98.03 0.19753 0.19547 0.23929 0.2151 RANDOM 22.654
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] -0.55 0.93 -1.23 0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.892 r_dihedral_angle_4_deg 17.698 r_dihedral_angle_3_deg 13.118 r_dihedral_angle_1_deg 6.037 r_long_range_B_refined 5.231 r_long_range_B_other 5.227 r_scangle_other 3.673 r_scbond_it 2.391 r_scbond_other 2.39 r_mcangle_it 2.161
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.892 r_dihedral_angle_4_deg 17.698 r_dihedral_angle_3_deg 13.118 r_dihedral_angle_1_deg 6.037 r_long_range_B_refined 5.231 r_long_range_B_other 5.227 r_scangle_other 3.673 r_scbond_it 2.391 r_scbond_other 2.39 r_mcangle_it 2.161 r_mcangle_other 2.161 r_angle_refined_deg 1.553 r_mcbond_it 1.473 r_mcbond_other 1.473 r_angle_other_deg 1.008 r_chiral_restr 0.098 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 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 7054 Nucleic Acid Atoms Solvent Atoms 218 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing