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ESTS1 phthalate ester degrading esterase from Sulfobacillus acidophilus at 1.22A
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), 0.5% Jeffamine ED-2001
Crystal Properties Matthews coefficient Solvent content 2.231794 44.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.71 α = 90 b = 107.71 β = 90 c = 44.402 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 2022-10-22 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 1.22 27.61 100 0.132 15.5 3.26 1117439
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 1.22 1.24 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 1.22 25.884 91892 4733 99.96 0.175 0.173 0.167 0.2037 0.2022 13.602
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] -0.584 -0.292 -0.584 1.895
RMS Deviations Key Refinement Restraint Deviation r_rigid_bond_restr 17.807 r_dihedral_angle_6_deg 16.06 r_dihedral_angle_3_deg 14.286 r_dihedral_angle_2_deg 9.602 r_scbond_it 6.557 r_scbond_other 6.554 r_dihedral_angle_1_deg 6.24 r_scangle_it 5.958 r_scangle_other 5.957 r_lrange_it 4.963
RMS Deviations Key Refinement Restraint Deviation r_rigid_bond_restr 17.807 r_dihedral_angle_6_deg 16.06 r_dihedral_angle_3_deg 14.286 r_dihedral_angle_2_deg 9.602 r_scbond_it 6.557 r_scbond_other 6.554 r_dihedral_angle_1_deg 6.24 r_scangle_it 5.958 r_scangle_other 5.957 r_lrange_it 4.963 r_lrange_other 4.775 r_mcangle_it 2.482 r_mcangle_other 2.482 r_mcbond_it 2.199 r_mcbond_other 2.199 r_angle_refined_deg 1.695 r_angle_other_deg 0.574 r_nbd_refined 0.23 r_symmetry_xyhbond_nbd_refined 0.205 r_symmetry_nbd_other 0.191 r_symmetry_nbd_refined 0.188 r_nbtor_refined 0.187 r_nbd_other 0.186 r_xyhbond_nbd_refined 0.159 r_chiral_restr 0.09 r_symmetry_nbtor_other 0.084 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2303 Nucleic Acid Atoms Solvent Atoms 232 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction CrysalisPro data scaling MOLREP phasing