8ZJ7

Terephthalate 1,2-cis-dihydrodioldehydrogenase/Decarboxylase in complex with 3,4-Dihydroxybenzoate and NAD.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.42950.2 M Potassium sodium tartrate tetrahydrate 20% w/v Polyethylene glycol 3,350 pH 7.4
Crystal Properties
Matthews coefficientSolvent content
2.7354.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.303α = 90
b = 98.148β = 90
c = 168.036γ = 90
Symmetry
Space GroupP 2 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2022-09-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.885ESRFID23-1

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.2616899.80.1160.1270.0520.99810.55.842519
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.262.31001.2571.3720.5430.6242.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2.6524.00142519213599.5480.1850.18130.251749.71
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]
-6.911.944-5.044
RMS Deviations
KeyRefinement Restraint Deviation
r_lrange_it49.141
r_lrange_other48.092
r_scangle_it19.689
r_scangle_other19.683
r_mcangle_it16.897
r_mcangle_other16.896
r_dihedral_angle_3_deg15.016
r_dihedral_angle_6_deg13.626
r_scbond_it13.065
r_scbond_other13.057
RMS Deviations
KeyRefinement Restraint Deviation
r_lrange_it49.141
r_lrange_other48.092
r_scangle_it19.689
r_scangle_other19.683
r_mcangle_it16.897
r_mcangle_other16.896
r_dihedral_angle_3_deg15.016
r_dihedral_angle_6_deg13.626
r_scbond_it13.065
r_scbond_other13.057
r_mcbond_it11.088
r_mcbond_other11.086
r_dihedral_angle_2_deg8.795
r_dihedral_angle_1_deg5.997
r_rigid_bond_restr5.594
r_dihedral_angle_other_2_deg1.763
r_angle_refined_deg1.502
r_angle_other_deg0.49
r_symmetry_xyhbond_nbd_refined0.4
r_symmetry_xyhbond_nbd_other0.266
r_symmetry_nbd_refined0.239
r_nbd_refined0.225
r_symmetry_nbd_other0.201
r_xyhbond_nbd_refined0.186
r_nbtor_refined0.168
r_nbd_other0.16
r_ncsr_local_group_50.099
r_ncsr_local_group_30.097
r_ncsr_local_group_10.096
r_ncsr_local_group_60.094
r_ncsr_local_group_20.093
r_ncsr_local_group_40.089
r_symmetry_nbtor_other0.08
r_chiral_restr0.068
r_metal_ion_refined0.035
r_bond_refined_d0.007
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9182
Nucleic Acid Atoms
Solvent Atoms122
Heterogen Atoms128

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
Aimlessdata scaling
MOLREPphasing