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ESTS1 phthalate ester degrading esterase from Sulfobacillus acidophilus in complex with p-nitrophenol
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 45.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.156 α = 90 b = 108.156 β = 90 c = 44.549 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 2022-09-29 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 1.5 25.98 100 0.13 14.7 3.19 47847
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 99.4 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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.5 23.427 47831 2365 99.939 0.128 0.1257 0.1766 0.1504 14.289
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] -0.098 -0.049 -0.098 0.319
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.031 r_dihedral_angle_3_deg 14.554 r_mcangle_it 7.451 r_mcangle_other 7.448 r_mcbond_it 7.32 r_mcbond_other 7.317 r_scangle_it 7.055 r_scangle_other 7.054 r_dihedral_angle_2_deg 6.764 r_lrange_it 6.394
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.031 r_dihedral_angle_3_deg 14.554 r_mcangle_it 7.451 r_mcangle_other 7.448 r_mcbond_it 7.32 r_mcbond_other 7.317 r_scangle_it 7.055 r_scangle_other 7.054 r_dihedral_angle_2_deg 6.764 r_lrange_it 6.394 r_lrange_other 6.261 r_dihedral_angle_1_deg 6.239 r_scbond_it 5.171 r_scbond_other 5.17 r_rigid_bond_restr 3.725 r_angle_refined_deg 1.392 r_angle_other_deg 0.498 r_nbd_refined 0.226 r_symmetry_xyhbond_nbd_refined 0.22 r_symmetry_nbd_other 0.187 r_symmetry_nbd_refined 0.187 r_nbtor_refined 0.18 r_nbd_other 0.172 r_xyhbond_nbd_refined 0.152 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.076 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.005 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2312 Nucleic Acid Atoms Solvent Atoms 206 Heterogen Atoms 103
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction CrysalisPro data scaling MOLREP phasing