☰ Navigation Tabs
Optimization of the in silico designed Kemp eliminase KE70 by computational design and directed evolution R4 8/5A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JCJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.3 292 0.1M Ammonium Nitrat, 20% PEG 3350, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 1.88 34.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.756 α = 90 b = 52.756 β = 90 c = 153.694 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray CCD 2008-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.939 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 1.4 50 97.9 0.058 0.053 57.28 20.5 43950 43027 14.63
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 1.4 1.42 100 0.243 0.211 13.6 23.1 2163
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 1JCJ 1.4 49.88 40785 2155 97.88 0.17492 0.17408 0.1727 0.1903 0.1883 RANDOM 14.627
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] 0.25 0.25 -0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.174 r_dihedral_angle_4_deg 14.869 r_dihedral_angle_3_deg 10.883 r_dihedral_angle_1_deg 5.928 r_sphericity_free 3.946 r_scangle_it 3.176 r_sphericity_bonded 2.384 r_scbond_it 2.123 r_mcangle_it 1.354 r_rigid_bond_restr 1.244
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.174 r_dihedral_angle_4_deg 14.869 r_dihedral_angle_3_deg 10.883 r_dihedral_angle_1_deg 5.928 r_sphericity_free 3.946 r_scangle_it 3.176 r_sphericity_bonded 2.384 r_scbond_it 2.123 r_mcangle_it 1.354 r_rigid_bond_restr 1.244 r_angle_refined_deg 1.133 r_mcbond_it 0.824 r_chiral_restr 0.071 r_bond_refined_d 0.007 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 1801 Nucleic Acid Atoms Solvent Atoms 166 Heterogen Atoms 17
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling