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PETaseSM14 from marine-sponge Streptomyces sp.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-A0A679PDB4-F1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 0.2 M Ammonium sulfate, 0.1 M MES monohydrate pH 6.5, 30% w/v Polyethylene glycol monomethyl ether 5,000
Crystal Properties Matthews coefficient Solvent content 2.11 41.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.983 α = 90 b = 96.983 β = 90 c = 44.815 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 DECTRIS EIGER2 XE 16M 2024-01-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.7133 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.425 83.99 100 0.999 8.9 21.3 45062
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.425 1.45 0.305
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 NONE 1.425 83.99 45061 2279 99.971 0.14 0.1363 0.2018 0.198 22.788
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] 0.167 0.084 0.167 -0.543
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.515 r_dihedral_angle_3_deg 13.218 r_dihedral_angle_2_deg 10.196 r_dihedral_angle_1_deg 6.789 r_lrange_it 6.108 r_rigid_bond_restr 5.932 r_scangle_it 5.827 r_scangle_other 5.825 r_scbond_it 5.697 r_scbond_other 5.695
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.515 r_dihedral_angle_3_deg 13.218 r_dihedral_angle_2_deg 10.196 r_dihedral_angle_1_deg 6.789 r_lrange_it 6.108 r_rigid_bond_restr 5.932 r_scangle_it 5.827 r_scangle_other 5.825 r_scbond_it 5.697 r_scbond_other 5.695 r_lrange_other 5.264 r_mcangle_it 3.296 r_mcangle_other 3.295 r_mcbond_it 3.051 r_mcbond_other 3.043 r_angle_refined_deg 1.623 r_angle_other_deg 0.575 r_symmetry_nbd_refined 0.275 r_nbd_refined 0.232 r_nbd_other 0.221 r_xyhbond_nbd_refined 0.211 r_symmetry_nbd_other 0.192 r_nbtor_refined 0.18 r_symmetry_xyhbond_nbd_refined 0.152 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.079 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.004 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1994 Nucleic Acid Atoms Solvent Atoms 296 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling REFMAC phasing