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ESTS1 phthalate ester degrading esterase from Sulfobacillus acidophilus in complex with monoethylhexyl phtahalate and 2-ethylhexanol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 293 Sodium Malonate, HEPES pH 7, Jeffamine ED-2001
Crystal Properties Matthews coefficient Solvent content 2.257173 45.54092
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.004 α = 90 b = 108.004 β = 90 c = 44.662 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL RIGAKU HyPix-6000HE 2023-08-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.9 25.955 100 0.191 10.5 3.01 39498
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.94 0.814 1.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.9 25.955 23664 1164 99.772 0.186 0.1842 0.1838 0.2172 0.2177 28.122
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] -0.004 -0.002 -0.004 0.014
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.376 r_dihedral_angle_3_deg 15.599 r_dihedral_angle_2_deg 14.521 r_dihedral_angle_1_deg 6.455 r_lrange_it 6.274 r_lrange_other 6.238 r_scangle_it 4.702 r_scangle_other 4.701 r_scbond_it 3.042 r_scbond_other 3.041
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.376 r_dihedral_angle_3_deg 15.599 r_dihedral_angle_2_deg 14.521 r_dihedral_angle_1_deg 6.455 r_lrange_it 6.274 r_lrange_other 6.238 r_scangle_it 4.702 r_scangle_other 4.701 r_scbond_it 3.042 r_scbond_other 3.041 r_mcangle_it 2.859 r_mcangle_other 2.859 r_mcbond_it 1.968 r_mcbond_other 1.968 r_angle_refined_deg 1.319 r_angle_other_deg 0.872 r_nbd_other 0.276 r_nbd_refined 0.225 r_symmetry_nbd_other 0.202 r_symmetry_nbd_refined 0.2 r_nbtor_refined 0.181 r_xyhbond_nbd_refined 0.176 r_symmetry_xyhbond_nbd_refined 0.141 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.061 r_bond_other_d 0.038 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2295 Nucleic Acid Atoms Solvent Atoms 70 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction CrysalisPro data scaling MOLREP phasing