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The Crystal Structure of dsPETase05 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 HEPES pH7.5, 25% PEG3,350
Crystal Properties Matthews coefficient Solvent content 2.11 41.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.066 α = 90 b = 67.273 β = 96.529 c = 85.446 γ = 90
Symmetry Space Group P 1 21 1
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 EIGER X 16M 2024-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.979191 SSRF BL02U1
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 1.948 35.93 99.9 0.979 6.5 3.9 33866
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 1.948 2 0.801
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 1.948 35.924 33835 1708 99.644 0.151 0.1485 0.1604 0.1954 0.2077 12.763
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] 0.669 0.966 -1.354 0.452
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.049 r_dihedral_angle_3_deg 9.845 r_dihedral_angle_2_deg 8.057 r_dihedral_angle_1_deg 6.918 r_lrange_it 4.624 r_lrange_other 4.268 r_scangle_it 2.75 r_scangle_other 2.75 r_mcangle_other 2.086 r_mcangle_it 2.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.049 r_dihedral_angle_3_deg 9.845 r_dihedral_angle_2_deg 8.057 r_dihedral_angle_1_deg 6.918 r_lrange_it 4.624 r_lrange_other 4.268 r_scangle_it 2.75 r_scangle_other 2.75 r_mcangle_other 2.086 r_mcangle_it 2.085 r_scbond_it 1.77 r_scbond_other 1.769 r_angle_refined_deg 1.539 r_mcbond_it 1.323 r_mcbond_other 1.296 r_angle_other_deg 0.539 r_nbd_refined 0.213 r_symmetry_nbd_other 0.209 r_symmetry_xyhbond_nbd_refined 0.205 r_xyhbond_nbd_refined 0.194 r_nbtor_refined 0.179 r_nbd_other 0.15 r_symmetry_xyhbond_nbd_other 0.142 r_symmetry_nbd_refined 0.111 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.073 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3794 Nucleic Acid Atoms Solvent Atoms 523 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MoRDa phasing