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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 3NPU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 292 0.1M NaCl, 20% PEG 3000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.51 50.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.135 α = 90 b = 83.331 β = 90 c = 129.203 γ = 90
Symmetry Space Group P 21 21 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 2009-07-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.975 ESRF ID14-4
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 1.79 50 99.6 0.091 0.095 28.7 9.5 53457 53243 19.03
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 1.8 1.86 99.1 0.31 0.29 5.9 8.4 5234
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 3NPU 1.79 50 50467 2703 99.18 0.1983 0.19697 0.1957 0.22313 0.2219 RANDOM 19.029
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] 0.25 -1.15 0.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.214 r_dihedral_angle_4_deg 12.76 r_dihedral_angle_3_deg 11.691 r_dihedral_angle_1_deg 7.008 r_scangle_it 3.579 r_scbond_it 2.194 r_angle_refined_deg 1.258 r_mcangle_it 1.16 r_mcbond_it 0.712 r_nbtor_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.214 r_dihedral_angle_4_deg 12.76 r_dihedral_angle_3_deg 11.691 r_dihedral_angle_1_deg 7.008 r_scangle_it 3.579 r_scbond_it 2.194 r_angle_refined_deg 1.258 r_mcangle_it 1.16 r_mcbond_it 0.712 r_nbtor_refined 0.298 r_nbd_refined 0.198 r_symmetry_vdw_refined 0.187 r_xyhbond_nbd_refined 0.123 r_symmetry_hbond_refined 0.094 r_chiral_restr 0.081 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3698 Nucleic Acid Atoms Solvent Atoms 217 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling