☰ Navigation Tabs
Terephthalate 1,2-cis-dihydrodioldehydrogenase/Decarboxylase in complex with 4-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 7.4 295 0.2 M Potassium sodium tartrate tetrahydrate
20% w/v Polyethylene glycol 3,350
pH 7.4
Crystal Properties Matthews coefficient Solvent content 2.61 53.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.831 α = 90 b = 94.332 β = 90 c = 168.433 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 2022-08-23 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) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.5 26.61 98.3 0.2 0.218 0.113 0.981 6.4 12.8 31086
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.58 87.1 0.56 0.61 0.898 2 9.7
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 20.001 31086 1613 98.931 0.24 0.2383 0.2594 0.2793 0.2986 0.786
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] -4.828 7.171 -2.343
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.353 r_dihedral_angle_6_deg 13.846 r_dihedral_angle_2_deg 10.192 r_lrange_it 8.94 r_lrange_other 8.756 r_dihedral_angle_1_deg 6.552 r_angle_refined_deg 1.485 r_angle_other_deg 0.514 r_rigid_bond_restr 0.454 r_nbd_refined 0.215
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.353 r_dihedral_angle_6_deg 13.846 r_dihedral_angle_2_deg 10.192 r_lrange_it 8.94 r_lrange_other 8.756 r_dihedral_angle_1_deg 6.552 r_angle_refined_deg 1.485 r_angle_other_deg 0.514 r_rigid_bond_restr 0.454 r_nbd_refined 0.215 r_xyhbond_nbd_refined 0.203 r_symmetry_nbd_other 0.202 r_nbd_other 0.181 r_nbtor_refined 0.166 r_symmetry_xyhbond_nbd_refined 0.165 r_symmetry_nbd_refined 0.137 r_ncsr_local_group_4 0.119 r_ncsr_local_group_5 0.116 r_ncsr_local_group_2 0.115 r_ncsr_local_group_6 0.114 r_ncsr_local_group_1 0.111 r_symmetry_xyhbond_nbd_other 0.108 r_ncsr_local_group_3 0.101 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.074 r_metal_ion_refined 0.07 r_scangle_it 0.056 r_scangle_other 0.056 r_scbond_it 0.04 r_scbond_other 0.04 r_bond_refined_d 0.007 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 9183 Nucleic Acid Atoms Solvent Atoms 220 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction Aimless data scaling MOLREP phasing