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Terephthalate 1,2-cis-dihydrodioldehydrogenase/Decarboxylase in complex with 2,5-Dihydroxybenzoate.
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 8 295 4% v/v Tacsimate pH 6.0
12% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.59 52.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.549 α = 90 b = 94.717 β = 90 c = 166.714 γ = 90
Symmetry Space Group P 2 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 RIGAKU HyPix-6000HE 2023-01-15 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) 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 2.65 27.23 99.8 0.993 6.9 7.1 40549
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 2.65 2.76 100 0.788 2.1
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 2.65 24.001 40475 2000 99.663 0.262 0.2604 0.3054 0.2949 0.3237 3.479
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] -2.439 3.645 -1.206
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.009 r_dihedral_angle_3_deg 14.377 r_dihedral_angle_6_deg 13.806 r_dihedral_angle_1_deg 6.183 r_lrange_it 4.122 r_lrange_other 4.01 r_rigid_bond_restr 3.649 r_angle_refined_deg 1.343 r_mcangle_it 1.128 r_mcangle_other 1.128
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.009 r_dihedral_angle_3_deg 14.377 r_dihedral_angle_6_deg 13.806 r_dihedral_angle_1_deg 6.183 r_lrange_it 4.122 r_lrange_other 4.01 r_rigid_bond_restr 3.649 r_angle_refined_deg 1.343 r_mcangle_it 1.128 r_mcangle_other 1.128 r_scangle_it 1.115 r_scangle_other 1.115 r_mcbond_it 0.682 r_mcbond_other 0.681 r_scbond_it 0.677 r_scbond_other 0.677 r_angle_other_deg 0.471 r_nbd_refined 0.232 r_symmetry_xyhbond_nbd_refined 0.214 r_symmetry_nbd_other 0.201 r_xyhbond_nbd_refined 0.197 r_nbtor_refined 0.165 r_nbd_other 0.165 r_symmetry_nbd_refined 0.158 r_metal_ion_refined 0.132 r_ncsr_local_group_4 0.125 r_ncsr_local_group_5 0.114 r_ncsr_local_group_1 0.105 r_ncsr_local_group_2 0.104 r_ncsr_local_group_6 0.101 r_ncsr_local_group_3 0.079 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.067 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9184 Nucleic Acid Atoms Solvent Atoms 121 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction Aimless data scaling MOLREP phasing