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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 6.5 292 0.2M NaNitrat, 0.1M Bis Tris-propane, 20% PEG 3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.3 46.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.595 α = 90 b = 53.518 β = 110.34 c = 81.702 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 2010-04-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 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 1.48 50 99.6 0.101 0.096 15.5 4.1 84488 84151 17.6
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 1.48 1.51 98.9 0.354 0.315 2.6 3.8 4147
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 1.48 50 78893 4150 98.77 0.1447 0.14331 0.1416 0.17017 0.1679 RANDOM 17.632
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] -0.36 -0.47 0.42 -0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.827 r_dihedral_angle_4_deg 16.494 r_dihedral_angle_3_deg 12.039 r_scangle_it 9.449 r_scbond_it 6.303 r_dihedral_angle_1_deg 6.027 r_mcangle_it 3.923 r_rigid_bond_restr 3.011 r_mcbond_it 2.726 r_angle_refined_deg 2.021
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.827 r_dihedral_angle_4_deg 16.494 r_dihedral_angle_3_deg 12.039 r_scangle_it 9.449 r_scbond_it 6.303 r_dihedral_angle_1_deg 6.027 r_mcangle_it 3.923 r_rigid_bond_restr 3.011 r_mcbond_it 2.726 r_angle_refined_deg 2.021 r_chiral_restr 0.322 r_bond_refined_d 0.025 r_gen_planes_refined 0.013 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3683 Nucleic Acid Atoms Solvent Atoms 263 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling