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In silico designed of an improved Kemp eliminase KE70 mutant 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 6 292 0.2M NH4Cl, MES, 20% PEG 6000 , VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.48 50.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.386 α = 90 b = 82.872 β = 90 c = 127.964 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 RIGAKU RAXIS IV++ mirrors 2010-06-24 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 2.14 50 99.9 0.081 0.056 24.2 7 31384 31353 28.9
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 2.15 2.23 98.9 0.394 0.309 2.9 5.5 3047
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 2.14 50 29719 1574 99.59 0.22164 0.21963 0.2209 0.25874 0.2591 RANDOM 28.924
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] 0.92 -2 1.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.557 r_dihedral_angle_3_deg 15.479 r_dihedral_angle_4_deg 14.076 r_dihedral_angle_1_deg 7.09 r_scangle_it 4.092 r_scbond_it 2.666 r_angle_refined_deg 1.636 r_mcangle_it 1.53 r_mcbond_it 0.982 r_nbtor_refined 0.295
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.557 r_dihedral_angle_3_deg 15.479 r_dihedral_angle_4_deg 14.076 r_dihedral_angle_1_deg 7.09 r_scangle_it 4.092 r_scbond_it 2.666 r_angle_refined_deg 1.636 r_mcangle_it 1.53 r_mcbond_it 0.982 r_nbtor_refined 0.295 r_symmetry_vdw_refined 0.245 r_nbd_refined 0.205 r_symmetry_hbond_refined 0.148 r_xyhbond_nbd_refined 0.129 r_chiral_restr 0.105 r_bond_refined_d 0.019 r_gen_planes_refined 0.007 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 3608 Nucleic Acid Atoms Solvent Atoms 77 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling