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Terephthalate 1,2-cis-dihydrodioldehydrogenase/Decarboxylase in complex with 3-Hydroxybenzoate.
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 0.2 M Potassium sodium tartrate tetrahydrate
20% w/v Polyethylene glycol 3,350
pH 7.4
Crystal Properties Matthews coefficient Solvent content 2.58 52.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.734 α = 90 b = 94.273 β = 90 c = 166.395 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 2022-12-14 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 2.9 26.429 99.8 0.974 5 9.4 30906
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 2.9 3.06 0.95 0.824 2 5.9
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 2.9 26.429 30793 1408 99.412 0.25 0.2489 0.2684 0.2823 0.2897 0.541
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] -2.006 2.563 -0.557
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.337 r_dihedral_angle_6_deg 13.351 r_dihedral_angle_2_deg 10.264 r_dihedral_angle_1_deg 6.376 r_rigid_bond_restr 5.724 r_angle_refined_deg 2.519 r_lrange_it 2.264 r_lrange_other 2.264 r_scangle_it 0.738 r_scangle_other 0.738
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.337 r_dihedral_angle_6_deg 13.351 r_dihedral_angle_2_deg 10.264 r_dihedral_angle_1_deg 6.376 r_rigid_bond_restr 5.724 r_angle_refined_deg 2.519 r_lrange_it 2.264 r_lrange_other 2.264 r_scangle_it 0.738 r_scangle_other 0.738 r_scbond_it 0.731 r_scbond_other 0.731 r_angle_other_deg 0.475 r_symmetry_xyhbond_nbd_refined 0.239 r_symmetry_nbd_refined 0.229 r_nbd_refined 0.217 r_symmetry_nbd_other 0.197 r_symmetry_xyhbond_nbd_other 0.191 r_xyhbond_nbd_refined 0.183 r_nbd_other 0.174 r_nbtor_refined 0.164 r_ncsr_local_group_3 0.098 r_ncsr_local_group_4 0.097 r_ncsr_local_group_6 0.097 r_ncsr_local_group_2 0.093 r_ncsr_local_group_1 0.092 r_ncsr_local_group_5 0.092 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.064 r_bond_refined_d 0.021 r_chiral_restr_other 0.012 r_metal_ion_refined 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9176 Nucleic Acid Atoms Solvent Atoms 87 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction Aimless data scaling MOLREP phasing