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ESTS1 phthalate ester degrading esterase from Sulfobacillus acidophilus
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 2.25 45.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.057 α = 90 b = 108.057 β = 90 c = 44.542 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 2022-07-29 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 1.55 25.95 100 0.171 6.5 2.93 47747
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 1.55 1.58 100 0.817 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 1.55 25.95 47728 2359 99.948 0.154 0.151 0.1462 0.2055 0.2023 15.315
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] -0.329 -0.165 -0.329 1.069
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.101 r_dihedral_angle_3_deg 15.894 r_dihedral_angle_2_deg 10.137 r_dihedral_angle_1_deg 6.04 r_lrange_it 5.304 r_scangle_it 5.276 r_scangle_other 5.274 r_lrange_other 5.224 r_rigid_bond_restr 4.886 r_scbond_it 4.453
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.101 r_dihedral_angle_3_deg 15.894 r_dihedral_angle_2_deg 10.137 r_dihedral_angle_1_deg 6.04 r_lrange_it 5.304 r_scangle_it 5.276 r_scangle_other 5.274 r_lrange_other 5.224 r_rigid_bond_restr 4.886 r_scbond_it 4.453 r_scbond_other 4.452 r_mcangle_other 3.051 r_mcangle_it 3.046 r_mcbond_it 2.486 r_mcbond_other 2.422 r_angle_refined_deg 1.458 r_symmetry_xyhbond_nbd_refined 0.5 r_angle_other_deg 0.493 r_nbd_other 0.291 r_symmetry_nbd_refined 0.255 r_nbd_refined 0.224 r_symmetry_nbd_other 0.188 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.152 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.075 r_xyhbond_nbd_other 0.009 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 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 213 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction CrysalisPro data scaling MOLREP phasing