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Crystal structure of the Lactobacillus johnsonii cinnamoyl esterase LJ0536 S106A mutant in complex with ethylferulate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Crystal structure of the Lactobacillus johnsonii cinnamoyl esterase LJ0536 S106A mutant
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298 0.1 M Tris pH 8.5, 0.2 M ammonium sulphate, 25% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.22 44.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.26 α = 90 b = 83.891 β = 98.21 c = 88.947 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 HTC mirrors 2009-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.58 50 73.1 0.046 31.21 2 52487 52487 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.58 1.61 21.6 0.26 3.09 1.3 769
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 Crystal structure of the Lactobacillus johnsonii cinnamoyl esterase LJ0536 S106A mutant 1.58 44.2 49803 2673 73.06 0.21609 0.2113 0.2177 0.30439 0.3079 RANDOM 26.599
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] 0.65 0.04 -1.61 0.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.66 r_dihedral_angle_4_deg 20.668 r_dihedral_angle_3_deg 15.05 r_dihedral_angle_1_deg 6.86 r_scangle_it 5.708 r_scbond_it 4.285 r_mcangle_it 2.393 r_rigid_bond_restr 2.268 r_angle_refined_deg 1.933 r_mcbond_it 1.698
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.66 r_dihedral_angle_4_deg 20.668 r_dihedral_angle_3_deg 15.05 r_dihedral_angle_1_deg 6.86 r_scangle_it 5.708 r_scbond_it 4.285 r_mcangle_it 2.393 r_rigid_bond_restr 2.268 r_angle_refined_deg 1.933 r_mcbond_it 1.698 r_chiral_restr 0.128 r_bond_refined_d 0.021 r_gen_planes_refined 0.01 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 r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3908 Nucleic Acid Atoms Solvent Atoms 907 Heterogen Atoms 52
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling