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ESTS1 phthalate ester degrading esterase from Sulfobacillus acidophilus in complex with Dimethyl phthalate
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 7 293.15 Sodium malonate, 0.1 M HEPES (pH 7.0), Jeffamine ED-2001
Crystal Properties Matthews coefficient Solvent content 2.234 44.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.668 α = 90 b = 107.668 β = 90 c = 44.489 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 2022-10-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 1.6 25.48 100 0.18 12.4 3.28 47379
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 100 1 1.2
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 1.6 25.48 39076 1848 99.959 0.15 0.1475 0.1842 0.194 0.2246 8.656
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] -0.047 -0.024 -0.047 0.153
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.785 r_dihedral_angle_6_deg 16.231 r_dihedral_angle_3_deg 14.646 r_dihedral_angle_1_deg 6.167 r_rigid_bond_restr 3.637 r_lrange_other 2.831 r_lrange_it 2.822 r_scangle_it 2.725 r_scangle_other 2.724 r_scbond_it 2.358
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.785 r_dihedral_angle_6_deg 16.231 r_dihedral_angle_3_deg 14.646 r_dihedral_angle_1_deg 6.167 r_rigid_bond_restr 3.637 r_lrange_other 2.831 r_lrange_it 2.822 r_scangle_it 2.725 r_scangle_other 2.724 r_scbond_it 2.358 r_scbond_other 2.357 r_mcangle_other 1.711 r_mcangle_it 1.701 r_angle_refined_deg 1.442 r_mcbond_it 1.335 r_mcbond_other 1.335 r_angle_other_deg 0.489 r_symmetry_nbd_refined 0.237 r_nbd_other 0.228 r_nbd_refined 0.222 r_symmetry_xyhbond_nbd_refined 0.214 r_symmetry_nbd_other 0.189 r_nbtor_refined 0.181 r_xyhbond_nbd_refined 0.171 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.074 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2313 Nucleic Acid Atoms Solvent Atoms 162 Heterogen Atoms 91
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction CrysalisPro data scaling MOLREP phasing