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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 15% PEG 8000, 17% glycerol, 150 mM MgCl2, 100 mM Tris pH 7.2. Seeding used to nucleate crystal formation.
Crystal Properties Matthews coefficient Solvent content 2.14 42.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.051 α = 90 b = 125.179 β = 101.97 c = 110.496 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 315 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 2.23 47.2 99.8 0.13 0.988 9.2 3.8 85391
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 2.23 2.27 99.1 0.739 0.654 2.3 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5kqt 2.23 47.2 81119 4237 99.74 0.16514 0.16374 0.1722 0.19198 0.1969 RANDOM 22.983
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] 0.16 -0.88 -0.35 0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.689 r_dihedral_angle_4_deg 17.287 r_dihedral_angle_3_deg 13.386 r_dihedral_angle_1_deg 5.926 r_long_range_B_refined 5.727 r_long_range_B_other 5.727 r_scangle_other 4.204 r_scbond_it 2.626 r_scbond_other 2.626 r_mcangle_it 2.531
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.689 r_dihedral_angle_4_deg 17.287 r_dihedral_angle_3_deg 13.386 r_dihedral_angle_1_deg 5.926 r_long_range_B_refined 5.727 r_long_range_B_other 5.727 r_scangle_other 4.204 r_scbond_it 2.626 r_scbond_other 2.626 r_mcangle_it 2.531 r_mcangle_other 2.531 r_mcbond_it 1.667 r_mcbond_other 1.665 r_angle_refined_deg 1.56 r_angle_other_deg 0.995 r_chiral_restr 0.092 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 14005 Nucleic Acid Atoms Solvent Atoms 564 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing