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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 4 mg/mL and reservoir conditions of 15% PEG 8000, 11 mM calcium acetate, 100 mM Tris pH 7.1. Microcrystals were used as nucleating agents to obtain full size crystals.
Crystal Properties Matthews coefficient Solvent content 2.42 49.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.451 α = 90 b = 102.538 β = 90 c = 199.781 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 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 2.1 48.6 99.6 0.17 0.994 9.5 7.3 59261
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 2.1 2.15 97.6 0.899 0.67 2.2 7.3
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 5kqt 2.1 48.6 56252 2892 99.36 0.20597 0.20425 0.2107 0.23987 0.2421 RANDOM 29.309
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 1.09 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.709 r_dihedral_angle_4_deg 14.233 r_dihedral_angle_3_deg 13.351 r_dihedral_angle_1_deg 7.245 r_long_range_B_refined 5.241 r_long_range_B_other 5.241 r_scangle_other 2.489 r_mcangle_it 2.176 r_mcangle_other 2.176 r_scbond_it 1.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.709 r_dihedral_angle_4_deg 14.233 r_dihedral_angle_3_deg 13.351 r_dihedral_angle_1_deg 7.245 r_long_range_B_refined 5.241 r_long_range_B_other 5.241 r_scangle_other 2.489 r_mcangle_it 2.176 r_mcangle_other 2.176 r_scbond_it 1.52 r_scbond_other 1.52 r_angle_refined_deg 1.424 r_mcbond_it 1.343 r_mcbond_other 1.34 r_angle_other_deg 0.953 r_chiral_restr 0.082 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 6957 Nucleic Acid Atoms Solvent Atoms 358 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing