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Evolutionary optimization of computationally designed enzymes: Kemp eliminases of the KE07 series
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IIP PDB ENTRY 3IIP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 Microbatch under oil 8 292 0.2M MgCl2, Tris pH8, 20% PEG6000, Microbatch under oil, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.41 48.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.77 α = 90 b = 82.324 β = 90 c = 175.4 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 IMAGE PLATE MAR scanner 345 mm plate 2007-11-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.954 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.8 50 98.1 52231
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.86 92.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB ENTRY 3IIP 1.8 50 50477 49518 2646 98.1 0.21127 0.20936 0.2099 0.24713 0.2475 RANDOM 19.886
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] 0.19 -0.33 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.619 r_dihedral_angle_4_deg 22.497 r_dihedral_angle_3_deg 13.786 r_dihedral_angle_1_deg 7.94 r_scangle_it 3.631 r_scbond_it 2.384 r_angle_refined_deg 1.507 r_mcangle_it 1.418 r_mcbond_it 0.952 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.619 r_dihedral_angle_4_deg 22.497 r_dihedral_angle_3_deg 13.786 r_dihedral_angle_1_deg 7.94 r_scangle_it 3.631 r_scbond_it 2.384 r_angle_refined_deg 1.507 r_mcangle_it 1.418 r_mcbond_it 0.952 r_nbtor_refined 0.309 r_nbd_refined 0.211 r_symmetry_vdw_refined 0.184 r_symmetry_hbond_refined 0.15 r_xyhbond_nbd_refined 0.145 r_chiral_restr 0.113 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 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 3962 Nucleic Acid Atoms Solvent Atoms 319 Heterogen Atoms 1
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling