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EstS1 esterase active site mutant S154A in complex with Bis(2-hydroxyethyl) terephthalate (BHET)
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, SITTING DROP 293.15 Sodium malonate, 0.1 M HEPES (pH 7.0), Jeffamine ED-2001
Crystal Properties Matthews coefficient Solvent content 2.20869827 44.3456879
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.502 α = 90 b = 106.502 β = 90 c = 44.945 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 2025-01-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54184
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim 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 2 27.55 100 0.102 0.037 22.3 15.04 19907
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 100 0.369 0.925 6.9 11.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 AlphaFold 2 22.482 19890 1008 99.91 0.181 0.1786 0.1787 0.2232 0.2235 12.487
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] 0.077 0.039 0.077 -0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.168 r_dihedral_angle_3_deg 14.317 r_dihedral_angle_2_deg 13.494 r_dihedral_angle_1_deg 6.357 r_lrange_it 6.019 r_scangle_it 3.549 r_scbond_it 2.247 r_mcangle_it 2.027 r_angle_refined_deg 1.853 r_mcbond_it 1.234
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.168 r_dihedral_angle_3_deg 14.317 r_dihedral_angle_2_deg 13.494 r_dihedral_angle_1_deg 6.357 r_lrange_it 6.019 r_scangle_it 3.549 r_scbond_it 2.247 r_mcangle_it 2.027 r_angle_refined_deg 1.853 r_mcbond_it 1.234 r_nbtor_refined 0.319 r_symmetry_nbd_refined 0.246 r_nbd_refined 0.236 r_symmetry_xyhbond_nbd_refined 0.217 r_xyhbond_nbd_refined 0.168 r_chiral_restr 0.12 r_gen_planes_refined 0.009 r_bond_refined_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2279 Nucleic Acid Atoms Solvent Atoms 95 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction CrysalisPro data scaling MOLREP phasing