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Optimization of the in silico designed Kemp eliminase KE70 by computational design and directed evolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JCJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 292 0.2M NaF, 0.1M Bis Tris Propane, 20% PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.28 46.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.222 α = 90 b = 53.295 β = 110.19 c = 81.846 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 IMAGE PLATE RIGAKU RAXIS IV++ mirros 2008-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 2.25 50 97.8 0.081 0.077 22.28 6.5 23599 51193 30.25
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.33 83.8 0.217 0.195 4.8 4.9 2034
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 1JCJ 2.25 50 22380 1207 97.28 0.19198 0.18927 0.1904 0.24116 0.231 RANDOM 30.257
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] 0.81 -1.22 0.14 -1.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.272 r_dihedral_angle_4_deg 17.007 r_dihedral_angle_3_deg 15.891 r_dihedral_angle_1_deg 7.94 r_scangle_it 4.105 r_scbond_it 2.672 r_angle_refined_deg 1.733 r_mcangle_it 1.515 r_mcbond_it 0.944 r_nbtor_refined 0.293
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.272 r_dihedral_angle_4_deg 17.007 r_dihedral_angle_3_deg 15.891 r_dihedral_angle_1_deg 7.94 r_scangle_it 4.105 r_scbond_it 2.672 r_angle_refined_deg 1.733 r_mcangle_it 1.515 r_mcbond_it 0.944 r_nbtor_refined 0.293 r_symmetry_vdw_refined 0.218 r_nbd_refined 0.199 r_symmetry_hbond_refined 0.198 r_xyhbond_nbd_refined 0.131 r_chiral_restr 0.122 r_bond_refined_d 0.02 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3651 Nucleic Acid Atoms Solvent Atoms 41 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling