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ESTS1 phthalate ester degrading esterase from Sulfobacillus acidophilus in complex with dimethyl phthalate on surface
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 45.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.038 α = 90 b = 108.038 β = 90 c = 44.546 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 2022-09-30 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 1.5 27.7 100 0.158 8.6 3.02 58638
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 1.5 1.53 100 1 1.3
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 1.5 25.562 47678 2351 99.878 0.154 0.1512 0.151 0.2002 0.2001 18.264
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] 0.702 0.351 0.702 -2.276
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.945 r_dihedral_angle_2_deg 15.741 r_dihedral_angle_3_deg 14.436 r_dihedral_angle_1_deg 6.049 r_rigid_bond_restr 3.41 r_lrange_it 2.664 r_lrange_other 2.651 r_scangle_it 2.595 r_scangle_other 2.594 r_scbond_it 2.281
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.945 r_dihedral_angle_2_deg 15.741 r_dihedral_angle_3_deg 14.436 r_dihedral_angle_1_deg 6.049 r_rigid_bond_restr 3.41 r_lrange_it 2.664 r_lrange_other 2.651 r_scangle_it 2.595 r_scangle_other 2.594 r_scbond_it 2.281 r_scbond_other 2.28 r_mcangle_other 1.763 r_mcangle_it 1.76 r_mcbond_it 1.448 r_mcbond_other 1.448 r_angle_refined_deg 1.425 r_angle_other_deg 0.49 r_nbd_other 0.233 r_nbd_refined 0.225 r_symmetry_xyhbond_nbd_refined 0.225 r_symmetry_nbd_refined 0.219 r_symmetry_nbd_other 0.191 r_nbtor_refined 0.182 r_xyhbond_nbd_refined 0.142 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.075 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 190 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction CrysalisPro data scaling MOLREP phasing