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Optimization of the in silico designed Kemp eliminase KE70 by computational design and directed evolution R2 3/5G
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 MICROBATCH 5.5 277 PCB pH5.0, PEG 1500, pH 5.5, Microbatch, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.45 49.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.008 α = 90 b = 96.228 β = 125.88 c = 71.274 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray IMAGE PLATE RIGAKU RAXIS IV++ mirror 2008-08-05 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 2.02 50 97.9 0.07 0.051 19.6 5.1 35683 34934 19.24
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 2.02 2.09 95.3 0.32 0.282 3.07 4.4 3420
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 2.02 50 33171 1757 97.85 0.20806 0.20521 0.2075 0.26019 0.2539 RANDOM 19.241
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] -0.39 -0.4 -0.28 0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.822 r_dihedral_angle_4_deg 14.889 r_dihedral_angle_3_deg 13.968 r_dihedral_angle_1_deg 6.211 r_scangle_it 3.648 r_scbond_it 2.326 r_angle_refined_deg 1.338 r_mcangle_it 1.304 r_mcbond_it 0.856 r_angle_other_deg 0.618
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.822 r_dihedral_angle_4_deg 14.889 r_dihedral_angle_3_deg 13.968 r_dihedral_angle_1_deg 6.211 r_scangle_it 3.648 r_scbond_it 2.326 r_angle_refined_deg 1.338 r_mcangle_it 1.304 r_mcbond_it 0.856 r_angle_other_deg 0.618 r_nbd_other 0.505 r_nbtor_refined 0.293 r_symmetry_vdw_refined 0.239 r_nbd_refined 0.204 r_xyhbond_nbd_refined 0.134 r_chiral_restr 0.093 r_symmetry_hbond_refined 0.065 r_bond_refined_d 0.016 r_bond_other_d 0.014 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 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 3640 Nucleic Acid Atoms Solvent Atoms 157 Heterogen Atoms 10
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling