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ESTS1 phthalate ester degrading esterase from Sulfobacillus acidophilus in complex with paranitrophenyl butyrate
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 2.259 45.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.048 α = 90 b = 108.048 β = 90 c = 44.672 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 2023-01-13 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 1.8 27.73 100 0.04 15.2 3.93 27832
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 1.8 1.84 100 1 2.4
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 1.8 23.404 27816 1276 99.928 0.125 0.1217 0.1217 0.1854 0.185 19.131
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] -0.15 -0.075 -0.15 0.486
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.601 r_dihedral_angle_6_deg 15.528 r_dihedral_angle_2_deg 10.318 r_lrange_it 6.666 r_scangle_it 6.516 r_scangle_other 6.514 r_lrange_other 6.462 r_dihedral_angle_1_deg 6.082 r_scbond_it 5.835 r_scbond_other 5.833
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.601 r_dihedral_angle_6_deg 15.528 r_dihedral_angle_2_deg 10.318 r_lrange_it 6.666 r_scangle_it 6.516 r_scangle_other 6.514 r_lrange_other 6.462 r_dihedral_angle_1_deg 6.082 r_scbond_it 5.835 r_scbond_other 5.833 r_mcangle_it 3.943 r_mcangle_other 3.943 r_rigid_bond_restr 3.283 r_mcbond_it 3.106 r_mcbond_other 3.091 r_angle_refined_deg 1.3 r_angle_other_deg 0.445 r_symmetry_nbd_refined 0.335 r_nbd_refined 0.229 r_symmetry_nbd_other 0.189 r_symmetry_xyhbond_nbd_refined 0.188 r_nbd_other 0.187 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.154 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.065 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2302 Nucleic Acid Atoms Solvent Atoms 151 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction CrysalisPro data scaling MOLREP phasing