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The Crystal Structure of dsPETase01 from Biortus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FX5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1M Tris-HCl pH8.5, 20% PEG6,000
Crystal Properties Matthews coefficient Solvent content 2.38 48.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.67 α = 90 b = 71.748 β = 90 c = 168.896 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS3 S 6M 2024-11-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 0.99999 SPring-8 BL45XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.4 44.291 99.9 0.102 24.9 13 105378
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.42 0.61
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 1.4 44.291 105278 5230 99.845 0.13 0.1293 0.1292 0.148 0.1479 10.433
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] 0.311 -0.266 -0.045
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.187 r_dihedral_angle_3_deg 10.361 r_dihedral_angle_2_deg 8.321 r_dihedral_angle_1_deg 6.181 r_lrange_it 5.66 r_lrange_other 4.848 r_scangle_it 3.013 r_scangle_other 3.013 r_scbond_other 1.99 r_scbond_it 1.989
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.187 r_dihedral_angle_3_deg 10.361 r_dihedral_angle_2_deg 8.321 r_dihedral_angle_1_deg 6.181 r_lrange_it 5.66 r_lrange_other 4.848 r_scangle_it 3.013 r_scangle_other 3.013 r_scbond_other 1.99 r_scbond_it 1.989 r_angle_refined_deg 1.897 r_mcangle_other 1.628 r_mcangle_it 1.626 r_mcbond_it 1.142 r_mcbond_other 1.073 r_angle_other_deg 0.644 r_symmetry_xyhbond_nbd_refined 0.271 r_xyhbond_nbd_refined 0.229 r_nbd_refined 0.222 r_symmetry_nbd_other 0.184 r_nbtor_refined 0.183 r_nbd_other 0.159 r_chiral_restr 0.104 r_symmetry_nbd_refined 0.102 r_symmetry_nbtor_other 0.083 r_symmetry_xyhbond_nbd_other 0.058 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3898 Nucleic Acid Atoms Solvent Atoms 839 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MoRDa phasing