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Crystal structure of the Lactobacillus johnsonii cinnamoyl esterase LJ0536 S106A mutant in complex with caffeic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PF8 PDB entry 3PF8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298 0.1 M TRIS, 0.2 M LITHIUM SULPHATE, 30% PEG4K, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.2 44.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.318 α = 90 b = 84.168 β = 97.56 c = 87.604 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 2010-01-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.54178
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 1.75 50 99.7 0.047 21.86 4.1 51281 51428 2
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 1.75 1.78 97.6 0.462 3.3 2520
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 PDB entry 3PF8 1.76 50 48659 2615 98.91 0.14596 0.14258 0.1498 0.20862 0.2155 RANDOM 35.29
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] -0.01 -1.03 -2.07 1.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.432 r_dihedral_angle_4_deg 21.877 r_dihedral_angle_3_deg 13.731 r_scangle_it 7.016 r_dihedral_angle_1_deg 6.059 r_scbond_it 4.945 r_mcangle_it 2.925 r_rigid_bond_restr 2.533 r_mcbond_it 1.901 r_angle_refined_deg 1.812
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.432 r_dihedral_angle_4_deg 21.877 r_dihedral_angle_3_deg 13.731 r_scangle_it 7.016 r_dihedral_angle_1_deg 6.059 r_scbond_it 4.945 r_mcangle_it 2.925 r_rigid_bond_restr 2.533 r_mcbond_it 1.901 r_angle_refined_deg 1.812 r_chiral_restr 0.132 r_bond_refined_d 0.023 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 3916 Nucleic Acid Atoms Solvent Atoms 432 Heterogen Atoms 42
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling