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ESTS1 phthalate ester degrading esterase from Sulfobacillus acidophilus in complex with Monomethyl 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 293.15 Sodium malonate, 0.1 M HEPES (pH 7.0), Jeffamine ED-2001
Crystal Properties Matthews coefficient Solvent content 2.26 45.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.984 α = 90 b = 107.984 β = 90 c = 44.782 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 2022-08-18 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) 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 2 27.74 100 0.143 18.8 2.8 20399
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 0.517 7.8
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2 25.95 20382 963 99.892 0.113 0.1082 0.201 0.1904 19.039
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] 0.589 0.295 0.589 -1.912
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.137 r_dihedral_angle_2_deg 15.774 r_dihedral_angle_3_deg 15.125 r_rigid_bond_restr 9.008 r_scangle_it 7.835 r_scangle_other 7.834 r_lrange_it 7.083 r_lrange_other 7.061 r_scbond_it 6.822 r_scbond_other 6.811
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.137 r_dihedral_angle_2_deg 15.774 r_dihedral_angle_3_deg 15.125 r_rigid_bond_restr 9.008 r_scangle_it 7.835 r_scangle_other 7.834 r_lrange_it 7.083 r_lrange_other 7.061 r_scbond_it 6.822 r_scbond_other 6.811 r_dihedral_angle_1_deg 6.516 r_mcangle_it 4.774 r_mcangle_other 4.773 r_mcbond_it 3.99 r_mcbond_other 3.969 r_angle_refined_deg 1.672 r_angle_other_deg 0.576 r_nbd_refined 0.227 r_symmetry_nbd_other 0.194 r_symmetry_nbd_refined 0.184 r_nbtor_refined 0.181 r_nbd_other 0.18 r_xyhbond_nbd_refined 0.154 r_symmetry_xyhbond_nbd_refined 0.118 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.081 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 r_bond_other_d 0.004 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2279 Nucleic Acid Atoms Solvent Atoms 115 Heterogen Atoms 67
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction CrysalisPro data scaling MOLREP phasing