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Optimization of the in silico designed Kemp eliminase KE70 by computational design and directed evolution R5 7/4A
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 4.6 277 0.2M (NH4)2SO4, 0.1M NaAC-3H2O, 30% PEG MME 2000, pH 4.6, Microbatch, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.4 48.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.524 α = 90 b = 64.725 β = 104.69 c = 49.032 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 100 IMAGE PLATE RIGAKU RAXIS IV++ Mirrors 2009-08-12 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 1.7 50 95.8 0.131 0.113 14.5 5.2 30127 28862 26.17
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 1.7 1.73 92.4 0.37 0.378 2.6 3.5 1358
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 1.7 50 27408 1451 95.76 0.20638 0.20484 0.2061 0.23364 0.2393 RANDOM 26.171
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] -0.48 1.01 -0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.561 r_dihedral_angle_4_deg 12.211 r_dihedral_angle_3_deg 11.809 r_dihedral_angle_1_deg 10.73 r_sphericity_free 7.048 r_rigid_bond_restr 5.425 r_scbond_it 5.394 r_scangle_it 4.86 r_sphericity_bonded 4.571 r_mcangle_it 1.656
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.561 r_dihedral_angle_4_deg 12.211 r_dihedral_angle_3_deg 11.809 r_dihedral_angle_1_deg 10.73 r_sphericity_free 7.048 r_rigid_bond_restr 5.425 r_scbond_it 5.394 r_scangle_it 4.86 r_sphericity_bonded 4.571 r_mcangle_it 1.656 r_angle_refined_deg 1.436 r_mcbond_it 1.039 r_chiral_restr 0.122 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1822 Nucleic Acid Atoms Solvent Atoms 124 Heterogen Atoms 9
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling